Publications

Abstract

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Authors: Natalie J Stanford, Katherine Wolstencroft, Martin Golebiewski, Renate Kania, Nick Juty, Christopher Tomlinson, Stuart Owen, Sarah Butcher, Henning Hermjakob, Nicolas Le Novère, Wolfgang Mueller, Jacky Snoep, Carole Goble

Date Published: 8th Dec 2015

Publication Type: Journal

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually extracted from the literature and data directly submitted from lab experiments. The database content includes kinetic parameters in relation to biochemical reactions and their biological sources with no restriction on any particular set of organisms. Additionally, kinetic rate laws and corresponding equations as well as experimental conditions are represented. All the data are manually curated and annotated by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language), e.g. for import in modelling tools.

Authors: U. Wittig, R. Kania, M. Golebiewski, M. Rey, L. Shi, L. Jong, E. Algaa, A. Weidemann, H. Sauer-Danzwith, S. Mir, O. Krebs, M. Bittkowski, E. Wetsch, I. Rojas, W. Muller

Date Published: 22nd Nov 2011

Publication Type: Journal

Abstract

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Authors: Katherine Wolstencroft, Olga Krebs, Jacky L. Snoep, Natalie J. Stanford, Finn Bacall, Martin Golebiewski, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, David D. van Niekerk, Alan R. Williams, Lars Malmström, Bernd Rinn, Wolfgang Müller, Carole Goble

Date Published: 3rd Jan 2017

Publication Type: Journal

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting the computational modeling to create models of biochemical reaction networks. SABIO-RK data are mainly extracted from literature but also directly submitted from lab experiments. In most cases the information in the literature is distributed across the whole publication, insufficiently structured and often described without standard terminology. Therefore the manual extraction of knowledge from the literature requires biological experts to understand the paper and interpret the data. The database offers the literature data in a structured format including annotations to controlled vocabularies, ontologies and external databases which supports modellers, as well as experimentalists, in the very time consuming process of collecting information from different publications. Here we describe the data extraction and curation efforts needed for SABIO-RK and give recommendations for publishing kinetic data in a complete and structured manner.

Authors: Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller

Date Published: 1st May 2014

Publication Type: Journal

Abstract (Expand)

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create models of biochemical reaction networks and to obtain a better understanding of the processes in living cells. To extract the knowledge from the literature, biocurators are required to understand a paper and interpret the data. For modellers, as well as experimentalists, this process is very time consuming because the information is distributed across the publication and, in most cases, is insufficiently structured and often described without standard terminology. In recent years, biological databases for different data types have been developed. The advantages of these databases lie in their unified structure, searchability and the potential for augmented analysis by software, which supports the modelling process. We have developed the SABIO-RK database for biochemical reaction kinetics. In the present review, we describe the challenges for database developers and curators, beginning with an analysis of relevant publications up to the export of database information in a standardized format. The aim of the present review is to draw the experimentalist's attention to the problem (from a data integration point of view) of incompletely and imprecisely written publications. We describe how to lower the barrier to curators and improve this situation. At the same time, we are aware that curating experimental data takes time. There is a community concerned with making the task of publishing data with the proper structure and annotation to ontologies much easier. In this respect, we highlight some useful initiatives and tools.

Authors: U. Wittig, M. Rey, R. Kania, M. Bittkowski, L. Shi, M. Golebiewski, A. Weidemann, W. Muller, I. Rojas

Date Published: 30th Oct 2013

Publication Type: Journal

Abstract (Expand)

BACKGROUND: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. RESULTS: The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. CONCLUSION: The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.

Authors: K. Wolstencroft, S. Owen, O. Krebs, Q. Nguyen, N. J. Stanford, M. Golebiewski, A. Weidemann, M. Bittkowski, L. An, D. Shockley, J. L. Snoep, W. Mueller, C. Goble

Date Published: 15th Jul 2015

Publication Type: Journal

Abstract (Expand)

Transcription is one of the basic processes of gene expression, controlled by a complex network of biochemical reactions. Despite its importance, most work on the visualisation of biochemical networks focuses on the representation of metabolic pathways. The visualisation of the complex networks controlling transcription requires the implementation of a hierarchical approach that allows the display of the structure of each regulatory region with its transcription factors and regulated operons. This paper presents a web-based application for the visualisation of transcriptional control networks. It takes as case study the organism Escherichia coli. The definition of the visual components implemented is mainly based on those proposed by Shen-Orr et al., 2002, slightly extended to visualise complex networks.

Authors: N. Sosa, A. Kremling, E. Ratsch, I. Rojas

Date Published: 28th Oct 2004

Publication Type: Journal

Abstract (Expand)

The Author-Review-Execute (A-R-E) is an innovative concept to offer under a single principle and platform an environment to support the life cycle of an (executable) paper; namely the authoring of the paper, its submission, the reviewing process, the author's revisions, its publication, and finally the study (reading/interaction) of the paper as well as extensions (follow ups) of the paper. It combines Semantic Wiki technology, a resolver that solves links both between parts of documents to executable code or to data, an anonymizing component to support the authoring and reviewing tasks, and web services providing link perennity.

Authors: Wolfgang Müller, Isabel Rojas, Andreas Eberhart, Peter Haase, Michael Schmidt

Date Published: 2011

Publication Type: Journal

Abstract (Expand)

A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrument to browser. The approach is based on two interrelated databases: the existing SABIO-RK database, containing kinetic data and corresponding metadata, and the newly introduced experimental raw data repository, MeMo-RK. Both systems are publicly available by web browser and web service interfaces and are configurable to ensure privacy of unpublished data. Users of this system are provided with the ability to view both kinetic parameters and the experimental raw data from which they are calculated, providing increased confidence in the data. A data analysis and submission tool, the kineticswizard, has been developed to allow the experimentalist to perform data collection, analysis and submission to both data resources. The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques.

Authors: N. Swainston, M. Golebiewski, H. L. Messiha, N. Malys, R. Kania, S. Kengne, O. Krebs, S. Mir, H. Sauer-Danzwith, K. Smallbone, A. Weidemann, U. Wittig, D. B. Kell, P. Mendes, W. Muller, N. W. Paton, I. Rojas

Date Published: 27th Aug 2010

Publication Type: Journal

Abstract (Expand)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such annotations support the definition of cross links to other related databases and augment the semantics of the data stored in the database.

Authors: I. Rojas, M. Golebiewski, R. Kania, O. Krebs, S. Mir, A. Weidemann, U. Wittig

Date Published: 14th Sep 2007

Publication Type: Journal

Abstract (Expand)

Enormous amounts of data result from genome sequencing projects and new experimental methods. Within this tremendous amount of genomic data 30-40 per cent of the genes being identified in an organism remain unknown in terms of their biological function. As a consequence of this lack of information the overall schema of all the biological functions occurring in a specific organism cannot be properly represented. To understand the functional properties of the genomic data more experimental data must be collected. A pathway database is an effort to handle the current knowledge of biochemical pathways and in addition can be used for interpretation of sequence data. Some of the existing pathway databases can be interpreted as detailed functional annotations of genomes because they are tightly integrated with genomic information. However, experimental data are often lacking in these databases. This paper summarises a list of pathway databases and some of their corresponding biological databases, and also focuses on information about the content and the structure of these databases, the organisation of the data and the reliability of stored information from a biological point of view. Moreover, information about the representation of the pathway data and tools to work with the data are given. Advantages and disadvantages of the analysed databases are pointed out, and an overview to biological scientists on how to use these pathway databases is given.

Authors: U. Wittig, A. De Beuckelaer

Date Published: 24th Jul 2001

Publication Type: Journal

Abstract (Expand)

Data quality in biological databases has become a topic of great discussion. To provide high quality data and to deal with the vast amount of biochemical data, annotators and curators need to be supported by software that carries out part of their work in an (semi-) automatic manner. The detection of errors and inconsistencies is a part that requires the knowledge of domain experts, thus in most cases it is done manually, making it very expensive and time-consuming. This paper presents two tools to partially support the curation of data on biochemical pathways. The tool enables the automatic classification of chemical compounds based on their respective SMILES strings. Such classification allows the querying and visualization of biochemical reactions at different levels of abstraction, according to the level of detail at which the reaction participants are described. Chemical compounds can be classified in a flexible manner based on different criteria. The support of the process of data curation is provided by facilitating the detection of compounds that are identified as different but that are actually the same. This is also used to identify similar reactions and, in turn, pathways.

Authors: U. Wittig, A. Weidemann, R. Kania, C. Peiss, I. Rojas

Date Published: 17th Jul 2008

Publication Type: Journal

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Authors: E. Ratsch, J. Schultz, J. Saric, P. C. Lavin, U. Wittig, U. Reyle, I. Rojas

Date Published: 17th Jul 2008

Publication Type: Journal

Abstract (Expand)

In this paper we aim at presenting the main flavours and uses that are given to the term ontology in the bio-domains. The paper does not intend to be a thorough review of the existing work in the area. It highlights the uses that are given to ontologies in the Scientific Databases and Visualisation Group at EML Research, in Heidelberg.

Authors: I. Rojas, E. Ratsch, J. Saric, U. Wittig

Date Published: 20th Apr 2004

Publication Type: Journal

Abstract (Expand)

To provide support for the analysis of biochemical pathways a database system based on a model that represents the characteristics of the domain is needed. This domain has proven to be difficult to model by using conventional data modelling techniques. We are building an ontology for biochemical pathways, which acts as the basis for the generation of a database on the same domain, allowing the definition of complex queries and complex data representation. The ontology is used as a modelling and analysis tool which allows the expression of complex semantics based on a first-order logic representation language. The induction capabilities of the system can help the scientist in formulating and testing research hypotheses that are difficult to express with the standard relational database mechanisms. An ontology representing the shared formalisation of the knowledge in a scientific domain can also be used as data integration tool clarifying the mapping of concepts to the developers of different databases. In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system.

Authors: I. Rojas, L. Bernardi, E. Ratsch, R. Kania, U. Wittig, J. Saric

Date Published: 18th Jun 2002

Publication Type: Journal

Abstract (Expand)

In systems biology, quantitative experimental data is the basis of building mathematical models. In most of the cases, they are stored in Excel files and hosted locally. To have a public database for collecting, retrieving and citing experimental raw data as well as experimental conditions is important for both experimentalists and modelers. However, the great effort needed in the data handling procedure and in the data submission procedure becomes the crucial limitation for experimentalists to contribute to a database, thereby impeding the database to deliver its benefit. Moreover, manual copy and paste operations which are commonly used in those procedures increase the chance of making mistakes. Excemplify, a web-based application, proposes a flexible and adaptable template-based solution to solve these problems. Comparing to the normal template based uploading approach, which is supported by some public databases, rather than predefining a format that is potentiall impractical, Excemplify allows users to create their own experiment-specific content templates in different experiment stages and to build corresponding knowledge bases for parsing. Utilizing the embedded knowledge of used templates, Excemplify is able to parse experimental data from the initial setup stage and generate following stages spreadsheets automatically. The proposed solution standardizes the flows of data traveling according to the standard procedures of applying the experiment, cuts down the amount of manual effort and reduces the chance of mistakes caused by manual data handling. In addition, it maintains the context of meta-data from the initial preparation manuscript and improves the data consistency. It interoperates and complements RightField and SEEK as well.

Authors: L. Shi, L. Jong, U. Wittig, P. Lucarelli, M. Stepath, S. Mueller, L. A. D'Alessandro, U. Klingmuller, W. Muller

Date Published: 4th Apr 2013

Publication Type: Journal

Abstract (Expand)

SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.

Authors: A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gabdoulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, R. Wade, U. Kummer

Date Published: 13th Jun 2008

Publication Type: Journal

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Authors: Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White, Seung Yon Rhee

Date Published: 4th Sep 2008

Publication Type: Journal

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Authors: Maksim Zakhartsev, Irina Medvedeva, Yury Orlov, Ilya Akberdin, Olga Krebs, Waltraud X. Schulze

Date Published: 1st Dec 2016

Publication Type: Journal

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Authors: S. D. Kügler, K. Polsterer, M. Hoecker

Date Published: 1st Apr 2015

Publication Type: Journal

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Authors: N. Gianniotis, S. D. Kügler, P. Tino, K. L. Polsterer, R. Misra

Date Published: 1st May 2015

Publication Type: InProceedings

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Authors: K. L. Polsterer, F. Gieseke, N. Gianniotis, S. D. Kuegler

Date Published: 1st Aug 2015

Publication Type: Journal

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Authors: S. D. Kügler, N. Gianniotis, K. L. Polsterer

Date Published: 25th Jun 2015

Publication Type: Journal

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Authors: K. L. Polsterer, F. Gieseke, C. Igel

Date Published: 1st Sep 2015

Publication Type: InProceedings

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Authors: A. R. López-Sánchez, W. P. Maksym, K. L. Polsterer, K. Borden, R. P. Hollow, L. Whyte

Date Published: 25th Sep 2015

Publication Type: Journal

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Authors: Maximilian Hoecker, Kai Lars Polsterer, Sven Dennis Kugler, Vincent Heuveline

Date Published: 1st Oct 2015

Publication Type: InProceedings

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Authors: F. Miczek, F. K. Röpke, P. V. F. Edelmann

Date Published: 1st Apr 2015

Publication Type: Journal

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Authors: Kai S. Marquardt, Stuart A. Sim, Ashley J. Ruiter, Ivo R. Seitenzahl, Sebastian T. Ohlmann, Markus Kromer, Rüdiger Pakmor, Friedrich K. Röpke

Date Published: 1st Aug 2015

Publication Type: Journal

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Authors: M. Kromer, S. T. Ohlmann, R. Pakmor, A. J. Ruiter, W. Hillebrandt, K. S. Marquardt, F. K. Röpke, I. R. Seitenzahl, S. A. Sim, S. Taubenberger

Date Published: 1st Jul 2015

Publication Type: Journal

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Authors: C. Inserra, S. A. Sim, L. Wyrzykowski, S. J. Smartt, M. Fraser, M. Nicholl, K. J. Shen, A. Jerkstrand, A. Gal-Yam, D. A. Howell, K. Maguire, P. Mazzali, S. Valenti, S. Taubenberger, S. Benitez-Herrera, D. Bersier, N. Blagorodnova, H. Campbell, T.-W. Chen, N. Elias-Rosa, W. Hillebrandt, Z. Kostrzewa-Rutkowska, S. Kozłowski, M. Kromer, J. D. Lyman, J. Polshaw, F. K. Röpke, A. J. Ruiter, K. Smith, S. Spiro, M. Sullivan, O. Yaron, D. Young, F. Yuan

Date Published: 20th Jan 2015

Publication Type: Journal

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Authors: C. Travaglio, R. Gallino, T. Rauscher, F. K. Röpke, W. Hillebrandt

Date Published: 20th Jan 2015

Publication Type: Journal

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Authors: Ivo R. Seitenzahl, Matthias Herzog, Ashley J. Ruiter, Kai Marquardt, Sebastian T. Ohlmann, Friedrich K. Röpke

Date Published: 1st Dec 2015

Publication Type: Journal

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Authors: Joel de Jesús Mendoza-Temis, Meng-Ru Wu, Karlheinz Langanke, Gabriel Martínez-Pinedo, Andreas Bauswein, Hans-Thomas Janka

Date Published: 1st Nov 2015

Publication Type: Journal

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Authors: Roland Diehl, Thomas Siegert, Wolfgang Hillebrandt, Martin Krause, Jochen Greiner, Keiichi Maeda, Friedrich K. Röpke, Stuart A. Sim, Wei Wang, Xiaoling Zhang

Date Published: 28th Jan 2015

Publication Type: Journal

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Authors: Y.-C. Pan, R. J. Foley, M. Kromer, O. D. Fox, W. Zheng, P. Challis, K. I. Clubb, A. V. Filippenko, G. Folatelli, M. L. Graham, W. Hillebrandt, R. P. Kirshner, W. H. Lee, R. Pakmor, F. Patat, M. M. Phillips, G. Pignata, F. Röpke, I. Seitenzahl, J. M. Silverman, J. D. Simon, A. Sternberg, M. D. Stritzinger, S. Taubenberger, J. Vinko, J. C. Wheeler

Date Published: 12th Aug 2015

Publication Type: Journal

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Authors: Zheng-Wei Liu, T. M. Tauris, F. K. Röpke, T. J. Moriya, M. Kruckow, R. J. Stancliffe, R. G. Izzard

Date Published: 1st Dec 2015

Publication Type: Journal

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Authors: S. Baran, S. Lerch

Date Published: 2015

Publication Type: Journal

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Authors: W. Ehm, T. Gneiting, A. Jordan, F.. Krueger

Date Published: 2016

Publication Type: Journal

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Authors: K. Feldmann, M. Scheuerer, T. L. Thorarinsdottir

Date Published: 2015

Publication Type: Journal

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Authors: L. V. Hansen, T. L. Thorarinsdottir, E. Ovcharov, T. Gneiting, D. Richards

Date Published: 2015

Publication Type: Journal

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Author: Stephan Hemri

Date Published: 2019

Publication Type: InCollection

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Authors: S. Hemri, D. Lisniak, B. Klein

Date Published: 2015

Publication Type: Journal

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Author: E. Ovcharov

Date Published: 2015

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Authors: D. Richardson, S. Hemri, K. Bogner, T. Gneiting, T. Haiden, F. Pappenberger, M. Scheuerer

Date Published: 2014

Publication Type: Journal

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Author: R. Schefzik

Date Published: 2015

Publication Type: Journal

Abstract (Expand)

Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models.

Authors: Katherine Wolstencroft, Stuart Owen, Olga Krebs, Quyen Nguyen, Natalie J Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lihua An, David Shockley, Jacky L. Snoep, Wolfgang Mueller, Carole Goble

Date Published: 1st Dec 2015

Publication Type: Journal

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Authors: Philipp Gerstner, Michael Schick, Vincent Heuveline

Date Published: 2015

Publication Type: Journal

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Authors: Maximilian Hoecker, Kai Lars Polsterer, Sven Dennis Kugler, Vincent Heuveline

Date Published: 2015

Publication Type: InProceedings

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Authors: Nico Meyer-Hübner, Michael Suriyah, Thomas Leibfried, Viktor Slednev, Valentin Bertsch, Wolf Fichtner, Philipp Gerstner, Michael Schick, Vincent Heuveline

Date Published: 2015

Publication Type: InProceedings

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Authors: Chen Song, Michael Schick, Vincent Heuveline

Date Published: 2015

Publication Type: InProceedings

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Authors: Jonas Kratzke, Michael Schick, Vincent Heuveline

Date Published: 2015

Publication Type: Journal

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Authors: Jonas Kratzke, Nicolai Schoch, Christian Weis, Matthias Mueller-Eschner, Stefanie Speidel, Mina Farag, Carsten Beller, Vincent Heuveline

Date Published: 2015

Publication Type: InProceedings

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Authors: Nicolai Schoch, Sandy Engelhardt, Norbert Zimmermann, Stefanie Speidel, Raffaele De Simone, Ivo Wolf, Vincent Heuveline

Date Published: 2015

Publication Type: InProceedings

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Authors: Michael Bromberger, Pascal Bastian, Jan-Philip Bergeest, Christian Conrad, Vincent Heuveline, Karl Rohr, Wolfgang Karl

Date Published: 1st Apr 2016

Publication Type: InProceedings

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Authors: Michael Bromberger, Wolfgang Karl, Vincent Heuveline

Date Published: 1st Apr 2016

Publication Type: InProceedings

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Authors: Michael Bromberger, Wolfgang Karl, Vincent Heuveline

Date Published: 2015

Publication Type: InProceedings

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Authors: T Flouri, F Izquierdo-Carrasco, D Darriba, AJ Aberer, L-T Nguyen, BQ Minh, A Von Häseler, A Stamatakis

Date Published: 2015

Publication Type: Journal

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Authors: Michael J. Sanderson, Michelle M. McMahon, Alexandros Stamatakis, Derrick J. Zwickl, Mike Steel

Date Published: 17th Aug 2015

Publication Type: Journal

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Authors: Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon YW Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, others

Date Published: 2015

Publication Type: Journal

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Authors: Alexey M. Kozlov, Andre J. Aberer, Alexandros Stamatakis

Date Published: 25th Jul 2015

Publication Type: Journal

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Authors: Kassian Kobert, Leonidas Salichos, Antonis Rokas, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

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Authors: Adam D. Leaché, Barbara L. Banbury, Joseph Felsenstein, Adrián nieto-Montes de Oca, Alexandros Stamatakis

Date Published: 14th Oct 2015

Publication Type: Journal

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Authors: Andre J. Aberer, Alexandros Stamatakis, Fredrik Ronquist

Date Published: 14th Dec 2015

Publication Type: Journal

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Author: Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

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Authors: Tomáš Flouri, Kassian Kobert, Torbjørn Rognes, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

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Authors: Diego Darriba, Tomas Flouri, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

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In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by Thorne, Kishino, and Felsenstein in 1991. This paper has two parts. In the educational part, we cover teaching issues regarding the setup of the course and the practical and summarize student and teacher experiences. In the scientific part, the two student teams (Team I: Nikolai, Sebastian, Daniel; Team II: Sarah, Pierre) present their solutions for implementing efficient and numerically stable implementations of the TKF91 algorithm. The two teams worked independently on implementing the same algorithm. Hence, since the implementations yield identical results -with slight numerical deviations- we are confident that the implementations are correct. We describe the optimizations applied and make them available as open-source codes in the hope that our findings and software will be useful to the community as well as for similar programming practicals at other universities.

Authors: Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp, Daniel Opitz, Tomas Flouri, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

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Authors: Lucas Czech, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

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Authors: Emily Jane McTavish, Cody E. Hinchliff, James F. Allman, Joseph W. Brown, Karen A. Cranston, Mark T. Holder, Jonathan A. Rees, Stephen A. Smith

Date Published: 24th Aug 2015

Publication Type: Journal

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Authors: Emily Jane McTavish, David M Hillis

Date Published: 1st Dec 2015

Publication Type: Journal

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Authors: Emily Jane McTavish, Mike Steel, Mark T. Holder

Date Published: 1st Dec 2015

Publication Type: Journal

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Authors: Tomas Flouri, Emanuele Giaquinta, Kassian Kobert, Esko Ukkonen

Date Published: 1st Jun 2015

Publication Type: Journal

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Authors: Carl Barton, Tomáš Flouri, Costas S. Iliopoulos, Solon P. Pissis

Date Published: 1st May 2015

Publication Type: Journal

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Authors: Frauke Gräter, Wenjin Li

Date Published: 2015

Publication Type: InCollection

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Authors: David Peralta, Agnieszka K Bronowska, Bruce Morgan, Éva Dóka, Koen Van Laer, Péter Nagy, Frauke Gräter, Tobias P Dick

Date Published: 2015

Publication Type: Journal

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Authors: Anna Beckmann, Senbo Xiao, Jochen P Müller, Davide Mercadante, Timm Nüchter, Niels Kröger, Florian Langhojer, Wolfgang Petrich, Thomas W Holstein, Martin Benoit, others

Date Published: 2015

Publication Type: Journal

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Authors: Jing Zhou, Agnieszka Bronowska, Johanne Le Coq, Daniel Lietha, Frauke Gräter

Date Published: 2015

Publication Type: Journal

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Authors: Wenjin Li, Ilona B. Baldus, Frauke Gräter

Date Published: 2015

Publication Type: Journal

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Authors: Camilo Aponte-Santamarı́a, Volker Huck, Sandra Posch, Agnieszka K Bronowska, Sandra Graessle, Maria A Brehm, Tobias Obser, Reinhard Schneppenheim, Peter Hinterdorfer, Stefan W Schneider, others

Date Published: 2015

Publication Type: Journal

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Authors: Davide Mercadante, Sigrid Milles, Gustavo Fuertes, Dmitri I. Svergun, Edward A. Lemke, Frauke Gräter

Date Published: 2015

Publication Type: Journal

Abstract

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Authors: Johannes A. Wagner, Davide Mercadante, Ivana Nikić, Edward A. Lemke, Frauke Gräter

Date Published: 2015

Publication Type: Journal

Abstract

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Authors: Maxime Louet, Christian Seifert, Ulf Hensen, Frauke Gräter

Date Published: 2015

Publication Type: Journal

Abstract

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Authors: Sigrid Milles, Davide Mercadante, Iker Valle Aramburu, Malene Ringkjøbing Jensen, Niccolò Banterle, Christine Köhler, Swati Tyagi, Jane Clarke, Sarah L Shammas, Martin Blackledge, others

Date Published: 2015

Publication Type: Journal

Abstract

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Authors: Jing Zhou, Camilo Aponte-Santamaría, Sebastian Sturm, Jakob Tómas Bullerjahn, Agnieszka Bronowska, Frauke Gräter

Date Published: 2015

Publication Type: Journal

Abstract

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Authors: Antonio Disanto, S. Cavuoti, M. Brescia, C. Donalek, G. Longo, G. Riccio, S. G. Djorgovski

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Sven D. Kügler, Nikolaos Gianniotis, Kai L. Polsterer

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Kai L. Polsterer, Fabian Gieseke, Christian Igel, Bernd Doser, Nikolaos Gianniotis

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: E. Crawford, R. P. Norris, Kai L. Polsterer

Date Published: 1st Sep 2016

Publication Type: InProceedings

Abstract

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Author: Kai L. Polsterer

Date Published: 1st Oct 2016

Publication Type: Journal

Abstract

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Author: Antonio Disanto

Date Published: 1st Oct 2016

Publication Type: Journal

Abstract

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Authors: Kai L. Polsterer, Fabian Gieseke

Date Published: 1st Sep 2016

Publication Type: InProceedings

Abstract

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Author: Pierre Barbera

Date Published: 2016

Publication Type: Master's Thesis

Abstract

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Author: Diego Darriba

Date Published: 2016

Publication Type: Doctoral Thesis

Abstract

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Author: Kassian Kobert

Date Published: 2016

Publication Type: Doctoral Thesis

Abstract

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Author: Nikolaos Psonis

Date Published: 2016

Publication Type: Doctoral Thesis

Abstract

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Authors: Lucas Czech, Jaime Huerta-Cepas, Alexandros Stamatakis

Date Published: 22nd Mar 2017

Publication Type: Journal

Abstract

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Authors: Frédéric Mahé, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, David Singer, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cédric Berney, Alexey Kozlov, Edward A.D. Mitchell, Christophe V. W. Seppey, Elianne Egge, Guillaume Lentendu, Rainer Wirth, Gabriel Trueba, Micah Dunthorn

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Constantin Scholl, Kassian Kobert, Tomá Flouri, Alexandros Stamatakis

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: Diego Darriba, Michael Weiß, Alexandros Stamatakis

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba, Alexandros Stamatakis

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Eirini Skourtanioti, Paschalia Kapli, Çetin Ilgaz, Yusuf Kumlutaş, Aziz Avcı, Faraham Ahmadzadeh, Jelka Crnobrnja–Isailović, Iulian Gherghel, Petros Lymberakis, Nikos Poulakakis

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Faraham Ahmadzadeh, Morris Flecks, Miguel A. Carretero, Wolfgang Böhme, Flora Ihlow, Paschalia Kapli, Andreia Miraldo, Dennis Rödder

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Panagiotis Kornilios, Evanthia Thanou, Paschalia Kapli, Aristidis Parmakelis, Maria Chatzaki

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Susanne S Renner, Guido W Grimm, Paschalia Kapli, Thomas Denk

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Kassian Kobert, Alexandros Stamatakis, Tomáš Flouri

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé

Date Published: 1st Oct 2016

Publication Type: Journal

Abstract

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Authors: Alexey M Kozlov, Jiajie Zhang, Pelin Yilmaz, Frank Oliver Glöckner, Alexandros Stamatakis

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: P. Kapli, S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis, T. Flouri

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Xin Zhou, Paul B Frandsen, Ralph W Holzenthal, Clare R Beet, Kristi R Bennett, Roger J Blahnik, Núria Bonada, David Cartwright, Suvdtsetseg Chuluunbat, Graeme V Cocks, others

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Diep Thi Hoang, Le Sy Vinh, Tomas Flouri, Alexandros Stamatakis, Arndt von Häseler, Bui Quang Minh

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: S. Baran, S. Lerch

Date Published: 2016

Publication Type: Journal

Abstract

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Author: W. Ehm

Date Published: 11th Jul 2016

Publication Type: InCollection

Abstract

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Authors: W. Ehm, J. Wackermann

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Graham Elliott, Dalia Ghanem, Fabian Krüger

Date Published: 2016

Publication Type: Journal

Abstract

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Author: Jochen Fiedler

Date Published: 2016

Publication Type: Doctoral Thesis

Abstract

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Author: Stephan Hemri

Date Published: 2016

Publication Type: Doctoral Thesis

Abstract

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Authors: S. Hemri, T. Haiden, F. Pappenberger

Date Published: 2016

Publication Type: Journal

Abstract

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Author: Alexander Jordan

Date Published: 2016

Publication Type: Doctoral Thesis

Abstract

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Authors: F. Krüger, I. Nolte

Date Published: 2016

Publication Type: Journal

Abstract

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Author: Sebastian Lerch

Date Published: 2016

Publication Type: Doctoral Thesis

Abstract

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Author: R. Schefzik

Date Published: 2016

Publication Type: Journal

Abstract

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Author: R. Schefzik

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: T. Fissler, J. F. Ziegel, T. Gneiting

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Andreas Fetzer, Jasmin Metzger, Darko Katic, Keno März, Martin Wagner, Patrick Philipp, Sandy Engelhardt, Tobias Weller, Sascha Zelzer, Alfred M. Franz, Nicolai Schoch, Vincent Heuveline, Maria Maleshkova, Achim Rettinger, Stefanie Speidel, Ivo Wolf, Hannes Kenngott, Arianeb Mehrabi, Beat P. Müller-Stich, Lena Maier-Hein, Hans-Peter Meinzer, Marco Nolden

Date Published: 25th Mar 2016

Publication Type: Journal

Abstract

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Authors: Jonas Kratzke, Fabian Rengier, Christian Weis, Carsten J. Beller, Vincent Heuveline

Date Published: 22nd Mar 2016

Publication Type: Journal

Abstract

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Authors: Philipp Lösel, Vincent Heuveline

Date Published: 21st Mar 2016

Publication Type: Journal

Abstract

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Authors: N. Schoch, F. Kißler, M. Stoll, S. Engelhardt, R. de Simone, I. Wolf, R. Bendl, V. Heuveline

Date Published: 1st Jun 2016

Publication Type: Journal

Abstract

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Authors: Nicolai Schoch, Patrick Philipp, Tobias Weller, Sandy Engelhardt, Mykola Volovyk, Andreas Fetzer, Marco Nolden, Raffaele De Simone, Ivo Wolf, Maria Maleshkova, Achim Rettinger, Rudi Studer, Vincent Heuveline

Date Published: 18th Mar 2016

Publication Type: Journal

Abstract

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Authors: N. Schoch, S. Speidel, Y. Sure-Vetter, V. Heuveline

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: M. Wlotzka, V. Heuveline, S. Klatt, D. Kraus, E. Haas, K. Kiese, K. Butterbach-Bahl, P. Kraft, L. Breuer

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Svenja Lippok, Katra Kolšek, Achim Löf, Dennis Eggert, Willem Vanderlinden, Jochen P. Müller, Gesa König, Tobias Obser, Karoline Röhrs, Sonja Schneppenheim, Ulrich Budde, Carsten Baldauf, Camilo Aponte-Santamaría, Frauke Gräter, Reinhard Schneppenheim, Joachim O. Rädler, Maria A. Brehm

Date Published: 3rd Mar 2016

Publication Type: Journal

Abstract

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Authors: Sandra Posch, Camilo Aponte-Santamaría, Richard Schwarzl, Andreas Karner, Matthias Radtke, Frauke Gräter, Tobias Obser, Gesa König, Maria A. Brehm, Hermann J. Gruber, Roland R. Netz, Carsten Baldauf, Reinhard Schneppenheim, Robert Tampé, Peter Hinterdorfer

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Eduardo R. Cruz-Chú, Shijun Xiao, Sandeep P. Patil, Konstantinos Gkagkas, Frauke Gräter

Date Published: 20th Jan 2017

Publication Type: Journal

Abstract

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Authors: Davide Mercadante, Sigrid Milles, Gustavo Fuertes, Dmitri Svergun, Edward A Lemke, Frauke Gräter

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Ludivine Hocq, Fabien Sénéchal, Valérie Lefebvre, Arnaud Lehner, Jean-Marc Domon, Jean-Claude Mollet, Jérémy Dehors, Karine Pageau, Paulo Marcelo, François Guérineau, Katra Kolšek, Davide Mercadante, Jérôme Pelloux

Date Published: 1st Feb 2017

Publication Type: Journal

Abstract

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Authors: Christopher K. Dugard, Rachel A. Mertz, Catherine Rayon, Davide Mercadante, Christopher Hart, Matheus R. Benatti, Anna T. Olek, Phillip J. SanMiguel, Bruce R. Cooper, Wolf-Dieter Reiter, Maureen C. McCann, Nicholas C. Carpita

Date Published: 6th Jul 2016

Publication Type: Journal

Abstract

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Authors: Iker Valle Aramburu, Davide Mercadante, Sigrid Milles, Malene Ringkjøbing, Niccolò Banterle, Christine Koehler, Swati Tyagi, Jane Clarke, Sarah L Shammas, Martin Blackledge, others

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Anja Tursch, Davide Mercadante, Jutta Tennigkeit, Frauke Gräter, Suat Özbek

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Lisa M Kent, Trevor S Loo, Laurence D Melton, Davide Mercadante, Martin AK Williams, Geoffrey B Jameson

Date Published: 2016

Publication Type: Journal

Abstract

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Author: S. Kashif Sadiq

Date Published: 13th Nov 2016

Publication Type: Journal

Abstract

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Authors: Mario Gundić, Antonija Tomić, Rebecca C. Wade, Mihaela Matovina, Zrinka Karačić, Saša Kazazić, Sanja Tomić

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Rudi Tong, Rebecca C. Wade, Neil J. Bruce

Date Published: 1st Dec 2016

Publication Type: Journal

Abstract

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Authors: Daniela Schibich, Felix Gloge, Ina Pöhner, Patrik Björkholm, Rebecca C. Wade, Gunnar von Heijne, Bernd Bukau, Günter Kramer

Date Published: 1st Aug 2016

Publication Type: Journal

Abstract

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Authors: Musa Ozboyaci, Michael Martinez, Rebecca C. Wade

Date Published: 25th Aug 2016

Publication Type: Journal

Abstract

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Authors: Chiara Borsari, Rosaria Luciani, Cecilia Pozzi, Ina Poehner, Stefan Henrich, Matteo Trande, Anabela Cordeiro-da-Silva, Nuno Santarem, Catarina Baptista, Annalisa Tait, Flavio Di Pisa, Lucia Dello Iacono, Giacomo Landi, Sheraz Gul, Markus Wolf, Maria Kuzikov, Bernhard Ellinger, Jeanette Reinshagen, Gesa Witt, Philip Gribbon, Manfred Kohler, Oliver Keminer, Birte Behrens, Luca Costantino, Paloma Tejera Nevado, Eugenia Bifeld, Julia Eick, Joachim Clos, Juan Torrado, María D. Jiménez-Antón, María J. Corral, José M Alunda, Federica Pellati, Rebecca C. Wade, Stefania Ferrari, Stefano Mangani, Maria Paola Costi

Date Published: 10th Aug 2016

Publication Type: Journal

Abstract

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Authors: Daria B. Kokh, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Mehmet Ali Öztürk, Georgi V. Pachov, Rebecca C. Wade, Vlad Cojocaru

Date Published: 18th Aug 2016

Publication Type: Journal

Abstract

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Authors: Klemens Wild, Gert Bange, Domantas Motiejunas, Judith Kribelbauer, Astrid Hendricks, Bernd Segnitz, Rebecca C. Wade, Irmgard Sinning

Date Published: 1st Jul 2016

Publication Type: Journal

Abstract

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Authors: Antonia Stank, Stefan Richter, Rebecca C. Wade

Date Published: 21st Jul 2016

Publication Type: Journal

Abstract

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Authors: Sundar Raman Subramanian, Ettayapuram Ramaprasad Azhagiya Singam, Michael Berinski, Venkatesan Subramanian, Rebecca C. Wade

Date Published: 11th May 2016

Publication Type: Journal

Abstract

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Authors: Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovny, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan-Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie-Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphaël A.G. Chaleil, Paul A. Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra S. Negi, Zhiping Weng, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, Jinchao Yu, Françoise Ochsenbein, Raphaël Guerois, Anna Vangone, João P.G.L.M. Rodrigues, Gydo van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S.J. Melquiond, Koen Visscher, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Shen, Lenna X. Peterson, Hyung-Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodriguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jiménez-García, Iain H. Moal, Juan Férnandez-Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sandor Vajda, Scott Mottarella, David R. Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. Del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J. Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J. Wodak

Date Published: 1st Sep 2016

Publication Type: Journal

Abstract

Not specified

Authors: Antonia Stank, Daria B. Kokh, Jonathan C. Fuller, Rebecca C. Wade

Date Published: 15th Apr 2016

Publication Type: Journal

Abstract

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Authors: M. Ozboyaci, D. B. Kokh, R. C. Wade

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Xiaofeng Yu, Daria B. Kokh, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter, Rebecca C. Wade

Date Published: 2016

Publication Type: InCollection

Abstract

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Authors: Rafiullah Rafiullah, Muhammad Aslamkhan, Nagarajan Paramasivam, Christian Thiel, Ghulam Mustafa, Stefan Wiemann, Matthias Schlesner, Rebecca C Wade, Gudrun A Rappold, Simone Berkel

Date Published: 21st Jan 2016

Publication Type: Journal

Abstract (Expand)

Understanding protein–inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein–surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein–surface interactions and discuss the successes and limitations of current approaches.

Authors: Musa Ozboyaci, Daria B. Kokh, Stefano Corni, Rebecca C. Wade

Date Published: 2016

Publication Type: Journal

Abstract

Not specified

Authors: Khalid Mohammed Khan, Mohammad A. Mesaik, Omer M. Abdalla, Fazal Rahim, Samreen Soomro, Sobia A. Halim, Ghulam Mustafa, Nida Ambreen, Ahmad Shukralla Khalid, Muhammad Taha, Shahnaz Perveen, Muhammad Tanveer Alam, Abdul Hameed, Zaheer Ul-Haq, Hayat Ullah, Zia Ur Rehman, Rafat Ali Siddiqui, Wolfgang Voelter

Date Published: 1st Feb 2016

Publication Type: Journal

Abstract (Expand)

AbstractBackground Cytochrome {P450} sterol 14α-demethylase (CYP51) is an essential enzyme for sterol biosynthesis and a target for anti-parasitic drug design. However, the design of parasite-specific drugs that inhibit parasitic {CYP51} without severe side effects remains challenging. The active site of {CYP51} is situated in the interior of the protein. Here, we characterize the potential ligand egress routes and mechanisms in Trypanosoma brucei and human {CYP51} enzymes. Methods We performed Random Acceleration Molecular Dynamics simulations of the egress of four different ligands from the active site of models of soluble and membrane-bound T. brucei {CYP51} and of soluble human CYP51. Results In the simulations, tunnel 2 f, which leads to the membrane, was found to be the predominant ligand egress tunnel for all the ligands studied. Tunnels S, 1 and W, which lead to the cytosol, were also used in T. brucei CYP51, whereas tunnel 1 was the only other tunnel used significantly in human CYP51. The common tunnels found previously in other {CYPs} were barely used. The ligand egress times were shorter for human than T. brucei CYP51, suggesting lower barriers to ligand passage. Two gating residues, {F105} and M460, in T. brucei {CYP51} that modulate the opening of tunnels 2 f and S were identified. Conclusions Although the main egress tunnel was the same, differences in the tunnel-lining residues, ligand passage and tunnel usage were found between T. brucei and human CYP51s. General Significance The results provide a basis for the design of selective anti-parasitic agents targeting the ligand tunnels.

Authors: Xiaofeng Yu, Prajwal Nandekar, Ghulam Mustafa, Vlad Cojocaru, Galina I. Lepesheva, Rebecca C. Wade

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Benjamin Heinzerling, Alex Judea, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: Alex Judea, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: Mohsen Mesgar, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: Nafise Sadat Moosavi, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

Not specified

Authors: Nafise Sadat Moosavi, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: Daraksha Parveen, Mohsen Mesgar, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: Madeline Remse, Mohsen Mesgar, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

Not specified

Authors: Bernd Resch, Anja Summa, Peter Zeile, Michael Strube

Date Published: 6th Jun 2016

Publication Type: Journal

Abstract

Not specified

Authors: Anja Summa, Bernd Resch, Michael Strube

Date Published: 2016

Publication Type: InProceedings

Abstract

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Authors: Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath

Date Published: 14th Oct 2016

Publication Type: Journal

Abstract

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Authors: O. Krebs, K. Wolstencroft, NJ. Stanford, N. Morrison, M. Golebiewski, S. Owen, Q. Nguyen, JL. Snoep, W. Müller, C. Goble

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: David Nickerson, Koray Atalag, Bernard de Bono, Jörg Geiger, Carole Goble, Susanne Hollmann, Joachim Lonien, Wolfgang Müller, Babette Regierer, Natalie J. Stanford, Martin Golebiewski, Peter Hunter

Date Published: 6th Apr 2016

Publication Type: Journal

Abstract

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Authors: F. Schreiber, GD. Bader, P. Gleeson, M. Golebiewski, M. Hucka, Novère. Le, CJ. Myers, D. Nickerson, B. Sommer, D. Waltemath

Date Published: 2016

Publication Type: Journal

Abstract

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Authors: Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet, Charles Auffray

Date Published: 1st Dec 2016

Publication Type: Journal

Abstract

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Author: J. Wagner

Date Published: 1st May 2017

Publication Type: Journal

Abstract

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Authors: A. D’Isanto, K. L. Polsterer

Date Published: 2018

Publication Type: Journal

Abstract

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Authors: Fabian Gieseke, Kai Lars Polsterer, Ashish Mahabal, Christian Igel, Tom Heskes

Date Published: 1st Nov 2017

Publication Type: InProceedings

Abstract

Not specified

Author: Kai L. Polsterer

Date Published: 1st Oct 2016

Publication Type: InProceedings

Abstract

Not specified

Author: K. L. Polsterer

Date Published: 1st Sep 2017

Publication Type: InProceedings

Abstract

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Author: Nico Schwaiger

Date Published: 2017

Publication Type: Master's Thesis

Abstract

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Author: Sarah Lutteropp

Date Published: 2017

Publication Type: Master's Thesis

Abstract

Not specified

Authors: Cédric Berney, Andreea Ciuprina, Sara Bender, Juliet Brodie, Virginia Edgcomb, Eunsoo Kim, Jeena Rajan, Laura Wegener Parfrey, Sina Adl, Stéphane Audic, others

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, M Essex, Simon DW Frost, Astrid Gall, Simani Gaiseitsiwe, Mary Grabowski, Ronald Gray, others

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz von Looz, Antonis Rokas

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Tomas Flouri, Jiajie Zhang, Lucas Czech, Kassian Kobert, Alexandros Stamatakis

Date Published: 2017

Publication Type: InCollection

Abstract

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Authors: R. Biczok, P. Bozsoky, P. Eisenmann, J. Ernst, T. Ribizel, F. Scholz, A. Trefzer, F. Weber, M. Hamann, A. Stamatakis

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Benoit Morel, Tomas Flouri, Alexandros Stamatakis

Date Published: 1st Dec 2017

Publication Type: InProceedings

Abstract

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Authors: Sarah Bank, Manuela Sann, Christoph Mayer, Karen Meusemann, Alexander Donath, Lars Podsiadlowski, Alexey Kozlov, Malte Petersen, Lars Krogmann, Rudolf Meier, others

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Ralph S Peters, Lars Krogmann, Christoph Mayer, Alexander Donath, Simon Gunkel, Karen Meusemann, Alexey Kozlov, Lars Podsiadlowski, Malte Petersen, Robert Lanfear, others

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: J Šmíd, J Moravec, V Gvoždík, J Štundl, D Frynta, P Lymberakis, P Kapli, T Wilms, A Schmitz, M Shobrak, SH Yousefkhani, E Rastegar-Pouyani, AM Castilla, J Els, W Mayer

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Faraham Ahmadzadeh, Petros Lymberakis, Reyhaneh Saberi Pirouz, Paschalia Kapli

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: F Grímsson, P Kapli, C-C Hofmann, R Zetter, GW Grimm

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: W. Ehm, E. Ovcharov

Date Published: 2017

Publication Type: Journal

Abstract

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Author: T. Gneiting

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: S. Hemri, B. Klein

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: S. Lerch, S. Baran

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: S. Lerch, T. L. Thorarinsdottir, F. Ravazzolo, T. Gneiting

Date Published: 2017

Publication Type: Journal

Abstract

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Author: P. Schmidt

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Martin Baumann, Maria Effinger, Dirk Eller, Vincent Heuveline, Christian Kempf, Lukas Loos, Leonhard Maylein, Jörg Peltzer, Michelle Pfeiffer, Veit Probst, others

Date Published: 2017

Publication Type: Misc

Abstract

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Authors: Martin Baumann, Fabian Gehbart, Oliver Mattes, Sotirios Nikas, Vincent Heuveline

Date Published: 2017

Publication Type: Misc

Abstract

Not specified

Authors: Valentin Bertsch, Wolf Fichtner, Vincent Heuveline, Thomas Leibfried

Date Published: 2017

Publication Type: Misc

Abstract

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Authors: Lena Maier-Hein, S. Swaroop Vedula, Stefanie Speidel, Nassir Navab, Ron Kikinis, Adrian Park, Matthias Eisenmann, Hubertus Feussner, Germain Forestier, Stamatia Giannarou, Makoto Hashizume, Darko Katic, Hannes Kenngott, Michael Kranzfelder, Anand Malpani, Keno März, Thomas Neumuth, Nicolas Padoy, Carla M. Pugh, Nicolai Schoch, Danail Stoyanov, Russell H. Taylor, Martin Wagner, Gregory D. Hager, Pierre Jannin

Date Published: 2017

Publication Type: Journal

Abstract (Expand)

For real-time simulations of stiff models on electronic control units, one important ingredient is to reduce computation time within differentiation of the right-hand side of the underlying differential equation. A sparsing method represents a powerful tool in this context. For a reliable use of a real-time simulation of a stiff model in safety-critical conditions, it is important to be able to detect, when sparsing leads to an improper influence on the considered system. In this work we propose an extension which aims at addressing this numerically challenging problem in the context of real-time simulation.

Authors: Thomas Loderer, Vincent Heuveline

Date Published: 2017

Publication Type: Journal

Abstract (Expand)

Evolving our previous research results in the context of cognition-guidance and patient-specifity for simulation-enhanced cardiac surgery assistance, in this work we further investigate on (1) a machine learning framework which allows to patient-individually calibrate soft tissue material parameters for subsequent simulation, and (2) a profound knowledge management framework which may enhance the ontology-driven overall setup of the cognition-guided surgery simulation in a clinic environment. Rather than being a closed research work with an in-depth theory backup and a complete evaluation, we here present a technical report and some interesting experimental works that are to serve for further research and development.

Authors: Nicolai Schoch, Vincent Heuveline

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Simon Gawlok, Philipp Gerstner, Saskia Haupt, Vincent Heuveline, Jonas Kratzke, Philipp Lösel, Katrin Mang, Mareike Schmidtobreick, Nicolai Schoch, Nils Schween, Jonathan Schwegler, Chen Song, Martin Wlotzka

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Vincent Heuveline, Michael Schick, Clayton Webster, Peter Zaspel

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: S Klatt, D Kraus, P Kraft, L Breuer, M Wlotzka, V Heuveline, E Haas, R Kiese, Klaus Butterbach-Bahl

Date Published: 2017

Publication Type: Journal

Abstract (Expand)

Segmenting the blood pool and myocardium from a 3D cardiovascular magnetic resonance (CMR) image allows to create a patient-specific heart model for surgical planning in children with complex congenital heart disease (CHD). Implementation of semi-automatic or automatic segmentation algorithms is challenging because of a high anatomical variability of the heart defects, low contrast, and intensity variations in the images. Therefore, manual segmentation is the gold standard but it is labor-intensive. In this paper we report the set-up and results of a highly scalable semi-automatic diffusion algorithm for image segmentation. The method extrapolates the information from a small number of expert manually labeled reference slices to the remaining volume. While results of most semi-automatic algorithms strongly depend on well-chosen but usually unknown parameters this approach is parameter-free. Validation is performed on twenty 3D CMR images.

Authors: Philipp Lösel, Vincent Heuveline

Date Published: 2017

Publication Type: InCollection

Abstract

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Authors: Nico Meyer-Hübner, Michael Suriyah, Thomas Leibfried, Viktor Slednev, Valentin Bertsch, Wolf Fichtner, Philipp Gerstner, Michael Schick, Vincent Heuveline

Date Published: 2017

Publication Type: InCollection

Abstract

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Authors: Wolfgang Mexner, Matthias Bonn, Andreas Kopmann, Viktor Mauch, Doris Ressmann, Suren A. Chilingaryan, Nicholas Tan Jerome, Thomas Van De Kamp, Vincent Heuveline, Philipp Lösel, et al.

Date Published: 2018

Publication Type: Journal

Abstract

Not specified

Authors: N. Schoch, S. Engelhardt, R. De Simone, I. Wolf, V. Heuveline

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Nicolai Schoch, Vincent Heuveline

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Viktor Slednev, Manuel Ruppert, Valentin Bertsch, Wolf Fichtner, Nico Meyer-Hübner, Michael Suriyah, Thomas Leibfried, Philipp Gerstner, Michael Schick, Vincent Heuveline

Date Published: 2017

Publication Type: InCollection

Abstract

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Authors: Chen Song, Markus Stoll, Kristina Giske, Rolf Bendl, Vincent Heuveline

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Chen Song, Vincent Heuveline

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Martin Wlotzka, Vincent Heuveline

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Martin Wlotzka, Vincent Heuveline, Manuel F Dolz, M Reza Heidari, Thomas Ludwig, A Cristiano I Malossi, Enrique S Quintana-Orti

Date Published: 2017

Publication Type: InCollection

Abstract

Not specified

Authors: M. Wlotzka, V. Heuveline, S. Klatt, D. Kraus, E. Haas, R. Kiese, K. Butterbach-Bahl, P. Kraft, L. Breuer

Date Published: 2017

Publication Type: InCollection

Abstract

Not specified

Authors: M. Wlotzka, V. Heuveline

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: M. Wlotzka, T. Morel, A. Piacentini, V. Heuveline

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Sebastian Schmelzle, Thomas van de Kamp, Michael Heethoff, Vincent Heuveline, Philipp Lösel, Jürgen Becker, Felix Beckmann, Frank Schluenzen, Jörg U. Hammel, Andreas Kopmann, Wolfgang Mexner, Matthias Vogelgesang, Nicholas T. Jerome, Oliver Betz, Rolf Beutel, Benjamin Wipfler, Alexander Blanke, Steffen Harzsch, Marie Hörnig, Tilo Baumbach

Date Published: 7th Sep 2017

Publication Type: InProceedings

Abstract

Not specified

Authors: Davide Mercadante, Johannes A. Wagner, Iker V. Aramburu, Edward A. Lemke, Frauke Gräter

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Csaba Daday, Katra Kolšek, Frauke Gräter

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Camilo Aponte-Santamaría, Jan Brunken, Frauke Gräter

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Katra Kolšek, Camilo Aponte-Santamaría, Frauke Gräter

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: C Aponte-Santamarı́a, G Fischer, P Båth, R Neutze, BL de Groot

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: B Briones, C Aponte-Santamarı́a, BL de Groot

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Camilo Aponte-Santamaría, Svenja Lippok, Judith J. Mittag, Tobias Obser, Reinhard Schneppenheim, Carsten Baldauf, Frauke Gräter, Ulrich Budde, Joachim O. Rädler

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: Johannes A. Wagner, Sandeep P. Patil, Imke Greving, Marc Lämmel, Konstantinos Gkagkas, Tilo Seydel, Martin Müller, Bernd Markert, Frauke Gräter

Date Published: 2017

Publication Type: Journal

Abstract

Not specified

Authors: Gustavo Fuertes, Niccolò Banterle, Kiersten M. Ruff, Aritra Chowdhury, Davide Mercadante, Christine Koehler, Michael Kachala, Gemma Estrada Girona, Sigrid Milles, Ankur Mishra, Patrick R. Onck, Frauke Gräter, Santiago Esteban-Martín, Rohit V. Pappu, Dmitri I. Svergun, Edward A. Lemke

Date Published: 2017

Publication Type: Journal

Abstract

Not specified

Authors: Beifei Zhou, Philip J. Hogg, Frauke Gräter

Date Published: 2017

Publication Type: Journal

Abstract

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Author: S Sturm BI Costescu

Date Published: 2017

Publication Type: Journal

Abstract

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Authors: V Miletić, I Odorčić, P Nikolić, ŽM Svedružić

Date Published: 2017

Publication Type: Journal

Abstract (Expand)

Structure-based drug design has often been restricted by the rather static picture of protein–ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibilityy in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.

Authors: M. Amaral, D. B. Kokh, J. Bomke, A. Wegener, H. P. Buchstaller, H. M. Eggenweiler, P. Matias, C. Sirrenberg, R. C. Wade, M. Frech

Date Published: 1st Dec 2017

Publication Type: Journal

Abstract

Not specified

Authors: Flavio Di Pisa, Giacomo Landi, Lucia Dello Iacono, Cecilia Pozzi, Chiara Borsari, Stefania Ferrari, Matteo Santucci, Nuno Santarem, Anabela Cordeiro-da-Silva, Carolina Moraes, Laura Alcantara, Vanessa Fontana, Lucio Freitas-Junior, Sheraz Gul, Maria Kuzikov, Birte Behrens, Ina Pöhner, Rebecca Wade, Maria Costi, Stefano Mangani

Date Published: 1st Mar 2017

Publication Type: Journal

Abstract (Expand)

Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, that it is our task to change scientific research into open scientific research and commit to Open Science principles.

Authors: Andrea Farnham, Christoph Kurz, Mehmet Ali Öztürk, Monica Solbiati, Oona Myllyntaus, Jordy Meekes, Tra My Pham, Clara Paz, Magda Langiewicz, Sophie Andrews, Liisa Kanninen, Chantal Agbemabiese, Arzu Tugce Guler, Jeffrey Durieux, Sarah Jasim, Olivia Viessmann, Stefano Frattini, Danagul Yembergenova, Carla Marin Benito, Marion Porte, Anaïs Grangeray-Vilmint, Rafael Prieto Curiel, Carin Rehncrona, Tareq Malas, Flavia Esposito, Kristina Hettne

Date Published: 1st Dec 2017

Publication Type: Journal

Abstract

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Authors: Wiktoria Jedwabny, Joanna Panecka-Hofman, Edyta Dyguda-Kazimierowicz, Rebecca C. Wade, W. Andrzej Sokalski

Date Published: 1st Aug 2017

Publication Type: Journal

Abstract

Not specified

Authors: Pasquale Linciano, Alice Dawson, Ina Pöhner, David M. Costa, Monica S. Sá, Anabela Cordeiro-da-Silva, Rosaria Luciani, Sheraz Gul, Gesa Witt, Bernhard Ellinger, Maria Kuzikov, Philip Gribbon, Jeanette Reinshagen, Markus Wolf, Birte Behrens, Véronique Hannaert, Paul A. M. Michels, Erika Nerini, Cecilia Pozzi, Flavio di Pisa, Giacomo Landi, Nuno Santarem, Stefania Ferrari, Puneet Saxena, Sandra Lazzari, Giuseppe Cannazza, Lucio H. Freitas-Junior, Carolina B. Moraes, Bruno S. Pascoalino, Laura M. Alcântara, Claudia P. Bertolacini, Vanessa Fontana, Ulrike Wittig, Wolfgang Müller, Rebecca C. Wade, William N. Hunter, Stefano Mangani, Luca Costantino, Maria P. Costi

Date Published: 14th Sep 2017

Publication Type: Journal

Abstract (Expand)

Author summary The malaria parasite Plasmodium has two invasive forms that migrate across different tissue barriers, the ookinete and the very rapidly migrating sporozoite. Previous work has shown that the motility of these and related parasites (e.g. Toxoplasma gondii) depends on a highly dynamic actin cytoskeleton and retrograde flow of surface adhesins. These unusual actin dynamics are due to the divergent structure of protozoan actins and the actions of actin-binding proteins, which can have non-canonical functions in these parasites. Profilin is one of the most important and most investigated actin-binding proteins, which binds ADP-actin and catalyzes ADP-ATP exchange to then promote actin polymerization. Parasite profilins bind monomeric actin and contain an additional domain compared to canonical profilins. Here we show that this additional domain of profilin is critical for actin binding and rapid sporozoite motility but has little impact on the slower ookinete. Sporozoites of a parasite line carrying mutations in this domain cannot translate force production and retrograde flow into optimal parasite motility. Using molecular dynamics simulations, we find that differences between mutant parasites in their capacity to migrate can be traced back to a single hydrogen bond at the actin-profilin interface.

Authors: Catherine A. Moreau, Saligram P. Bhargav, Hirdesh Kumar, Katharina A. Quadt, Henni Piirainen, Léanne Strauss, Jessica Kehrer, Martin Streichfuss, Joachim P. Spatz, Rebecca C. Wade, Inari Kursula, Friedrich Frischknecht

Date Published: 26th May 2017

Publication Type: Journal

Abstract

Not specified

Authors: Nadinath B Nillegoda, Antonia Stank, Duccio Malinverni, Niels Alberts, Anna Szlachcic, Alessandro Barducci, Paolo De Los Rios, Rebecca C Wade, Bernd Bukau

Date Published: 15th May 2017

Publication Type: Journal

Abstract

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Authors: Mehmet Ali Öztürk, Vlad Cojocaru, Rebecca C. Wade

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Joanna Panecka-Hofman, Ina Pöhner, Francesca Spyrakis, Talia Zeppelin, Flavio Di Pisa, Lucia Dello Iacono, Alessio Bonucci, Antonio Quotadamo, Alberto Venturelli, Stefano Mangani, Maria Paola Costi, Rebecca C. Wade

Date Published: 1st Dec 2017

Publication Type: Journal

Abstract (Expand)

ARL13B encodes for the ADP-ribosylation factor-like 13B GTPase, which is required for normal cilia structure and Sonic hedgehog (Shh) signaling. Disruptions in cilia structure or function lead to a class of human disorders called ciliopathies. Joubert syndrome is characterized by a wide spectrum of symptoms, including a variable degree of intellectual disability, ataxia, and ocular abnormalities. Here we report a novel homozygous missense variant c.[223G>A] (p.(Gly75Arg) in the ARL13B gene, which was identified by whole-exome sequencing of a trio from a consanguineous family with multiple-affected individuals suffering from intellectual disability, ataxia, ocular defects, and epilepsy. The same variant was also identified in a second family. We saw a striking difference in the severity of ataxia between affected male and female individuals in both families. Both ARL13B and ARL13B-c.[223G>A] (p.(Gly75Arg) expression rescued the cilia length and Shh defects displayed by Arl13b hennin (null) cells, indicating that the variant did not disrupt either ARL13B function. In contrast, ARL13B-c.[223G>A] (p.(Gly75Arg) displayed a marked loss of ARL3 guanine nucleotide-exchange factor activity, with retention of its GTPase activities, highlighting the correlation between its loss of function as an ARL3 guanine nucleotide-exchange factor and Joubert syndrome.

Authors: Rafiullah Rafiullah, Alyssa B. Long, Anna A. Ivanova, Hazrat Ali, Simone Berkel, Ghulam Mustafa, Nagarajan Paramasivam, Matthias Schlesner, Stefan Wiemann, Rebecca C. Wade, Eugen Bolthauser, Martin Blum, Richard A. Kahn, Tamara Caspary, Gudrun A. Rappold

Date Published: 1st Dec 2017

Publication Type: Journal

Abstract (Expand)

A considerable number of approved drugs show non-equilibrium binding characteristics, emphasizing the potential role of drug residence times for in vivo efficacy. Therefore, a detailed understanding of the kinetics of association and dissociation of a target–ligand complex might provide crucial insight into the molecular mechanism-of-action of a compound. This deeper understanding will help to improve decision making in drug discovery, thus leading to a better selection of interesting compounds to be profiled further. In this review, we highlight the contributions of the Kinetics for Drug Discovery (K4DD) Consortium, which targets major open questions related to binding kinetics in an industry-driven public-private partnership.

Authors: Doris A. Schuetz, Wilhelmus Egbertus Arnout de Witte, Yin Cheong Wong, Bernhard Knasmueller, Lars Richter, Daria B. Kokh, S. Kashif Sadiq, Reggie Bosma, Indira Nederpelt, Laura H. Heitman, Elena Segala, Marta Amaral, Dong Guo, Dorothee Andres, Victoria Georgi, Leigh A. Stoddart, Steve Hill, Robert M. Cooke, Chris De Graaf, Rob Leurs, Matthias Frech, Rebecca C. Wade, Elizabeth Cunera Maria de Lange, Adriaan P. IJzerman, Anke Müller-Fahrnow, Gerhard F. Ecker

Date Published: 1st Jun 2017

Publication Type: Journal

Abstract

Not specified

Authors: Antonia Stank, Daria B. Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C. Wade

Date Published: 3rd Jul 2017

Publication Type: Journal

Abstract

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Authors: Leo Born, Mohsen Mesgar, Michael Strube

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Benjamin Heinzerling, Michael Strube, Chin-Yew Lin

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Benjamin Heinzerling, Nafise Sadat Moosavi, Michael Strube

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Dirk Hovy, Shannon Spruit, Margaret Mitchell, Emily M. Bender, Michael Strube, Hanna Wallach

Date Published: 2017

Publication Type: Proceedings

Abstract

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Authors: Alex Judea, Michael Strube

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Sadao Kurohashi, Michael Strube

Date Published: 2017

Publication Type: Proceedings

Abstract

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Authors: Nafise Sadat Moosavi, Michael Strube

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Nafise Sadat Moosavi, Michael Strube

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Mark-Christoph Müller, Florian Reitz, Nicolas Roy

Date Published: 2017

Publication Type: Journal

Abstract

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Author: Mark-Christoph Müller

Date Published: 2017

Publication Type: InCollection

Abstract

Not specified

Authors: S. Jones, R. Andrassy, S. Sandalski, A. Davis, P. Woodward, F. Herwig

Date Published: 16th Dec 2016

Publication Type: Journal

Abstract

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Authors: Pavel A. Denissenkov, Falk Herwig, Umberto Battino, Christian Ritter, Marco Pignatari, Samuel Jones, Bill Paxton

Date Published: 10th Jan 2017

Publication Type: Journal

Abstract

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Authors: S. Andrews, C. Fryer, W. P. Even, S. Jones, M. Pignatari, NuGrid Collaboration

Date Published: 2017

Publication Type: InProceedings

Abstract

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Authors: Michele Sasdelli, W. Hillebrandt, M. Kromer, E. E. O. Ishida, F. K. Röpke, S. A. Sim, R. Pakmor, I. R. Seitenzahl, M. Fink

Date Published: 27th Jan 2017

Publication Type: Journal

Abstract

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Authors: Sebastian T. Ohlmann, Friedrich K. Röpke, Rüdiger Pakmor, Volker Springel

Date Published: 1st Mar 2017

Publication Type: Journal

Abstract

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Authors: Warren P. Wright, James P. Kneller, Sebastian T. Ohlmann, Friedrich K. Röpke, Kate Scholberg, Ivo R. Seitenzahl

Date Published: 1st Feb 2017

Publication Type: Journal

Abstract

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Authors: Wasilij Barsukow, Philipp V. F. Edelmann, Christian Klingenberg, Fabian Miczek, Friedrich K. Röpke

Date Published: 1st Aug 2017