Gwyn SkonePublications

Publications

Doctoral Thesis:

Stratagems for Effective Function Evaluation in Computational Chemistry
Oxford, 2010

Papers:

Doing a Good Turn: The Use of Quaternions for Rotation in Molecular Docking
J. Chem. Inf. Model. 2013
Knowing When To Give Up: Early-Rejection Stratagems in Ligand Docking
J. Comput. Aided Mol. Des. 2009
Protein Structure Computation
Proc. FBIT 2007

Posters:

Basic Strategies for Molecular Docking with Scoring Functions
German Conf. Bioinf. 2008

Presentations:

Knowing When To Give Up: Sensible Evaluation in Virtual Screening for Drug Discovery
OUCL Cakes Talk. 2008
Protein Structure Computation
Proc. OUCL PRG Student Conf. 2006

Doing a Good Turn: The Use of Quaternions for Rotation in Molecular Docking

Gwyn Skone, Stephen Cameron, and Irina Voiculescu
Journal of Chemical Information and Modeling, 2013, 53(12):3367-3372.
DOI: 10.1021/ci4005139

Link

http://pubs.acs.org/doi/abs/10.1021/ci4005139

Abstract

Much work has been done on algorithms for structure-based drug modeling in silico, and almost all these systems have a core need for three-dimensional geometric models. The manipulation of these models, particularly their transformation from one position to another, is a substantial computational task with design questions of its own. Solid body rotation is an important part of these transformations, and we present here a careful comparison of two established techniques: Euler angles and quaternions. The relative superiority of the quaternion method when applied to molecular docking is demonstrated by practical experiment, as is the crucial importance of proper adjustment calculations in search methods.