Gwyn SkonePublications


Doctoral Thesis:

Stratagems for Effective Function Evaluation in Computational Chemistry
Oxford, 2010


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


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


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

Knowing When To Give Up: Early-Rejection Stratagems in Ligand Docking

Gwyn Skone, Irina Voiculescu, and Stephen Cameron
Journal of Computer-Aided Molecular Design, 2009, 23:715-724.
DOI: 10.1007/s10822-009-9296-x



Virtual screening is an important resource in the drug discovery community, of which protein-ligand docking is a significant part. Much software has been developed for this purpose, largely by biochemists and those in related disciplines, who pursue ever more accurate representations of molecular interactions. The resulting tools, however, are very processor-intensive. This paper describes some initial results from a project to review computational chemistry techniques for docking from a non-chemistry standpoint. An abstract blueprint for protein-ligand docking using empirical scoring functions is suggested, and this is used to discuss potential improvements. By introducing computer science tactics such as lazy function evaluation, dramatic increases to throughput can and have been realized using a real-world docking program. Naturally, they can be extended to any system that approximately corresponds to the architecture outlined.