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Modelling of solvation effects for brownian dynamics simulation of biomolecular recognition.

Abstract

Not specified

Authors: Neil J. Bruce, Daria B. Kokh, Musa Ozboyaci, Rebecca C. Wade

Date Published: 27th Mar 2015

Publication Type: InBook

Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE’s … aim is to act as a coordinator, facilitator, and resource for different standardization efforts whose domains of use cover related areas of the computational biology space. In this perspective article, we summarize COMBINE, its general organization, and the community standards and other efforts involved in it. Our goals are to help guide readers toward standards that may be suitable for their research activities, as well as to direct interested readers to relevant communities where they can best expect to receive assistance in how to develop interoperable computational models.

Authors: Michael Hucka, David Phillip Nickerson, Gary Bader, Frank T Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris John Myers, Falk Schreiber, Dagmar Waltemath, Nicolas Le Novère

Date Published: 24th Feb 2015

Publication Type: Journal

A Quick Guide for Building a Successful Bioinformatics Community.

Abstract (Expand)

"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play … a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The ’How To Guide’ for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).

Authors: Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg

Date Published: 5th Feb 2015

Publication Type: Journal

Chemical Shift and Coupling Constant Analysis of Dibenzyloxy Disulfides

Abstract (Expand)

Dialkoxy disulfides have found applications in the realm of organic synthesis as an S2 or alkoxy donor, under thermal and photolytic decompositions conditions, respectively. Spectrally, dibenzyloxy … disulfides possess an ABq in the 1H NMR, which can shift by over 1.1 ppm depending on the substituents present on the aromatic ring, as well as the solvent employed. The effect of the said substituents and solvent were analyzed and compared to the center of the ABq, geminal coupling, and the differences in chemical shifts of the individual doublets. Additionally, quantum-chemical calculations demonstrated the intramolecular H-bonding arrangement, found within the dibenzyloxy disulfides.

Authors: Eric G. Stoutenburg, Ganna Gryn’ova, Michelle L. Coote, Ronny Priefer

Date Published: 1st Feb 2015

Publication Type: Journal

Experimental Evidence for Competitive N-O and O-C Bond Homolysis in Gas-Phase Alkoxyamines

Abstract (Expand)

The extensive use of alkoxyamines in controlled radical polymerisation and polymer stabilisation is based on rapid cycling between the alkoxyamine (R1R2NOR3) and a stable nitroxyl radical (R1R2NO•) via … homolysis of the labile OC bond. Competing homolysis of the alkoxyamine NO bond has been predicted to occur for some substituents leading to production of aminyl and alkoxyl radicals. This intrinsic competition between the OC and NO bond homolysis processes has to this point been difficult to probe experimentally. Herein we examine the effect of local molecular structure on the competition between NO and OC bond cleavage in the gas phase by variable energy tandem mass spectrometry in a triple quadrupole mass spectrometer. A suite of cyclic alkoxyamines with remote carboxylic acid moieties (HOOCR1R2NOR3) were synthesised and subjected to negative ion electrospray ionisation to yield [M − H]− anions where the charge is remote from the alkoxyamine moiety. Collision-induced dissociation of these anions yield product ions resulting, almost exclusively, from homolysis of OC and/or NO bonds. The relative efficacy of NO and OC bond homolysis was examined for alkoxyamines incorporating different R3 substituents by varying the potential difference applied to the collision cell, and comparing dissociation thresholds of each product ion channel. For most R3 substituents, product ions from homolysis of the OC bond are observed and product ions resulting from cleavage of the NO bond are minor or absent. A limited number of examples were encountered however, where NO homolysis is a competitive dissociation pathway because the OC bond is stabilised by adjacent heteroatom(s) (e.g. R3 = CH2F). The dissociation threshold energies were compared for different alkoxyamine substituents (R3) and the relative ordering of these experimentally determined energies is shown to correlate with the bond dissociation free energies, calculated by ab initio methods. Understanding the structure-dependent relationship between these rival processes will assist in the design and selection of alkoxyamine motifs that selectively promote the desirable OC homolysis pathway.

Authors: David L. Marshall, Ganna Gryn'ova, Michelle L. Coote, Philip J. Barker, Stephen J. Blanksby

Date Published: 1st Feb 2015

Publication Type: Journal

Dynamics of CYP51: implications for function and inhibitor design

Abstract

Not specified

Authors: Xiaofeng Yu, Vlad Cojocaru, Ghulam Mustafa, Outi M. H. Salo-Ahen, Galina I. Lepesheva, Rebecca C. Wade

Date Published: 1st Feb 2015

Publication Type: Journal

Ten Simple Rules for Organizing an Unconference

Abstract

Not specified

Authors: Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood

Date Published: 29th Jan 2015

Publication Type: Journal

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