Filter and export

Publications

What is a Publication?
1579 Publications visible to you, out of a total of 1579
Peptides binding to the dimer interface of thymidylate synthase for the treatment of cancer

Abstract

Not specified

Authors: M. Paola Costi, Gaetano Marverti, Daniela Cardinale, Alberto Venturelli, Stefania Ferrari, Glauco Ponterini, Stefan Henrich, Outi Salo-Ahen, Rebecca C. Wade

Date Published: 2009

Publication Type: Misc

Protein–surface interactions: challenging experiments and computations

Abstract (Expand)

Abstract Protein–surface interactions are fundamental in natural processes, and have great potential for applications ranging from nanotechnology to medicine. A recent workshop highlighted the current … achievements and the main challenges in the field. Copyright © 2009 John Wiley & Sons, Ltd.

Authors: Ori Cohavi, Stefano Corni, Francesca De Rienzo, Rosa Di Felice, Kay E. Gottschalk, Martin Hoefling, Daria Kokh, Elisa Molinari, Gideon Schreiber, Alexander Vaskevich, Rebecca C. Wade

Date Published: 2009

Publication Type: Journal

Computational approaches to identifying and characterizing protein binding sites for ligand design

Abstract (Expand)

Abstract Given the three-dimensional structure of a protein, how can one find the sites where other molecules might bind to it? Do these sites have the properties necessary for high affinity binding? … Is this protein a suitable target for drug design? Here, we discuss recent developments in computational methods to address these and related questions. Geometric methods to identify pockets on protein surfaces have been developed over many years but, with new algorithms, their performance is still improving. Simulation methods show promise in accounting for protein conformational variability to identify transient pockets but lack the ease of use of many of the (rigid) shape-based tools. Sequence and structure comparison approaches are benefiting from the constantly increasing size of sequence and structure databases. Energetic methods can aid identification and characterization of binding pockets, and have undergone recent improvements in the treatment of solvation and hydrophobicity. The “druggability” of a binding site is still difficult to predict with an automated procedure. The methodologies available for this purpose range from simple shape and hydrophobicity scores to computationally demanding free energy simulations. Copyright © 2009 John Wiley & Sons, Ltd.

Authors: Stefan Henrich, Outi M. H. Salo-Ahen, Bingding Huang, Friedrich F. Rippmann, Gabriele Cruciani, Rebecca C. Wade

Date Published: 2009

Publication Type: Journal

Control of convergent yolk syncytial layer nuclear movement in zebrafish

Abstract

Not specified

Authors: Lara Carvalho, Jan Stühmer, Justin S Bois, Yannis Kalaidzidis, Virginie Lecaudey, Carl-Philipp Heisenberg

Date Published: 2009

Publication Type: Journal

Big data: The future of biocuration

Abstract

Not specified

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

LUCIFER status report: summer 2008

Abstract

Not specified

Authors: Holger Mandel, Walter Seifert, Reiner Hofmann, Marcus Jütte, Rainer Lenzen, Nancy Ageorges, Dominik Bomans, Peter Buschkamp, Ralf-Jürgen Dettmar, Carmen Feiz, Hans Gemperlein, André Germeroth, Lutz Geuer, Jochen Heidt, Volker Knierim, Werner Laun, Michael Lehmitz, Ulrich Mall, Peter Müller, Vianac Naranjo, Kai Polsterer, Andreas Quirrenbach, Ludwig Schäffner, Florian Schwind, Peter Weiser, Harald Weisz

Date Published: 15th Aug 2008

Publication Type: Journal

Classification of chemical compounds to support complex queries in a pathway database.

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

Powered by
 (v.1.14.2)
About HITS Publication SEEK | About HITS-Publication-SEEK | Funding and Programmes | Credits
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH