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

Basic Strategies for Molecular Docking with Scoring Functions

Gwyn Skone, Stephen Cameron, and Irina Voiculescu
At German Conference on Bioinformatics, Dresden, September 2008.


Poster PDF (1.41 MiB)


In recent years, the potential benefits from high-throughput virtual screening to the drug discovery community have been recognized, bringing an increase in the number of tools developed for this purpose. These programs have to process large quantities of data, searching for an optimal solution in a vast combinatorial range. This is particularly the case for protein-ligand docking 1. Proteins are sophisticated structures, with complicated ligand-interactions for which either molecule might reshape itself 2,3. Even the very limited flexibility model of rigid conformation lists requires a 7-dimensional exploration, and the functions for evaluating pose suitability can be quite complex to calculate 4.

This work brings a pure computer science approach to the field, hoping to improve the speed and accuracy of such tools by exploring principles of function evaluation in the context of an existing commercial docking program. We present some early results from this project, demonstrating a substantial reduction in run time and some improvement to ligand placement.


  1. Halperin, I., Ma, B., Wolfson, H., and Nussinov, R.: Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions. Proteins, 2002, 47, 409-443.
  2. Skone, G.S. and Cameron, S.A.: Protein Structure Computation. In: Proc. FBIT. 2007.
  3. Teodoro, M.L. and Kavraki, L.E.: Conformational Flexibility Models for the Receptor in Structure Based Drug Design. Curr. Pharm. Des. 2003, 9, 1635-1648.
  4. Warren, G.L., Webster Andrews, C., Capelli, A-M., Clarke, B., LaLonde, J., Lambert, M.H., Lindvall, M., Nevins, N., Semus, S.F., Senger, S., Tedesco, G., Wall, I.D., Woolven, J.M., Peishoff, C.E., and Head, M.S.: A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 2006, 49, 5912-5931.