protein-ligand docking

review

This workshop was held on 12th September 2007 at Manchester University. The workshop focused on two areas: protein-ligand docking using AutoDock; and structure quality assessment and validation techniques.

The aim of first part of the workshop was to introduce students to the docking package AutoDock which is able to perform docking studies with a flexible ligand and a partially flexible receptor. We were very pleased to have Dr Garrett Morris, one of the primary developers of AutoDock to come over from the Scripps Research Institute, San Diego (US) to run this part of the workshop. Dr Morris started the morning session by giving a lecture on how AutoDock works and the theory behind docking in general. This was followed by a hands-on session where the delegates were able to set up and analyse the docking of the HIV-1 Protease inhibitor Indinavir to 1HSG.

The aim of the second part of the workshop was to introduce tools and techniques for structure quality assessment and data validation. Following on from the morning session the structure of HIV-1 Protease was analysed. Dr Jawahar Swaminathan of EBI, Cambridge (UK) ran this part of the course. Following a brief lecture on the role of the EBI and an introduction to some of the tools being used in the session, participants were given a hands-on tutorial which introduced methods used for structure quality assessment, from geometric and data quality checks and ligand verification, through to the use of Protein Quaternary Structures (PQS) and PISA for assembly generation and assessment. Particular attention was paid to the appreciation and understanding of data quality indicators returned from the validation and analysis services. This session provided participants will hands-on experience in using data validation, assembly and interaction analysis tools offered by the EBI Macromolecular Structure Databases group.

downloads

docking
The AutoDock suite of programs and information on how to use AutoDock can be found on the following website: http://autodock.scripps.edu/.

The introducory lecture given by Dr Garrett Morris can be found here. The tutorial file used at the workshop can be found here and the official tutorial files for AutoDock (which may be more up to date) can be found on the AutoDock website.

validation
The introductory lecture given by Dr Jawahar Swaminathan can be found here, and the tutorial on analysing the structure of HIV-1 Protease can be found here. Further information regarding the techniques which were used in this part of the workshop can be found on the following websites (please note that since this workshop took place, the MSD group at EBI is now known as PDBe. As a result of this name change a number of websites have been changed, some of the updated websites are below):

Geometry and Stereochemistry: http://www.ebi.ac.uk/msd-as/MSDvalidate/
Protein-Protein Interfaces (PISA) and PQS: http://www.ebi.ac.uk/pdbe/prot_int/pistart.html and http://www.ebi.ac.uk/pdbe/pqs/index.html
Chemistry of Small Molecules: http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl
Ligand Interactions and Active Sites: http://www.ebi.ac.uk/pdbe-site/PDBeMotif and http://www.ebi.ac.uk/pdbe-site/PDBeSite
Residue Interactions: http://www.ebi.ac.uk/pdbe-as/PDBeTemplate
Critical Assessment of PRediction of Interactions (CAPRI): http://capri.ebi.ac.uk/
Protein Databank in Europe Group: http://www.ebi.ac.uk/pdbe