Biological macromolecules and their ligands

Techniques in X-ray structure analysis and Docking

Report Workshop of the TeachSG Specific Support Action

Prague, June 10-11 2007

The workshop was designed to give protein crystallographers a good background on proper geometry definitions for ligands in protein-ligand complexes, to help crystallographers use properly the up-to-date tools for ligand searching in electron density, automated or semi-autometed ligand building and refinement and to provide some theoretical and practical training in order to apply the current computational techniques of docking when experimental data on complexes are missing.

The workshop was organized in two days, four lectures covering the background and examples of the individual techniques and four practical tutorials at Linux PCs. Four speakers/tutors provided valuable teaching and practical guidance through real applications of the computational methods, namely in use of the CCP4 package and web-based services for proper ligand geometry definitions, ArpWarp in ligand search, Coot in ligand search and model building and analysis and Autodock in ligand docking.

Fifteen participants benefited from the Workshop program, some of them already involved in projects focused on structures of complexes of proteins with important ligands and some at the very beginning of their scientific career gaining the first practical skills in model and ligand
building. There were many positive responses from the individual participants already during the course and the acquired knowledge and
skills were immediately used in their own projects. 

Printed handouts with the tutors’ notes and compiled CDs with Workshop notes and example input files were provided to the Workshop participants.

Workshop program

Sunday 10th June	Lectures, Masarykova kolej
13:00 – 13:30	Registration
13:30 – 13:35	Introductory remarks,Jan Dohnálek, IMC Prague
Short motivation remarks
13:35 – 13:40	Saccharides in antibodies,Petr Kolenko, IMC Prague
13:40 – 13:45	Correct building of glycoproteins, Max Crispin, University of Oxford
Workshop lectures
13:45 - 14:45	Databases, geometry parameters, ligand libraries and proper refinement (CSD, Relibase, HicUP, ProDRG, CCP4 sketcher and others), Garib Murshudov, YSBL York
14:45 – 15:45	ArpWarp – automated ligand fitting, principles and insights, Gerrit Langer, Guillaume Evrard, EMBL Hamburg
15:45 – 16:15	Coffee break
16:15 – 17:15	Coot and search for ligands in electron density maps, Bernhard Lohkamp, Karolinska Institutet, Stockholm
17:15 – 18:15	Docking, Pingping Guan, John Innes Centre, Norwich
19:30	Workshop dinner (walking distance from the venue)

Monday 11th June	Tutorials (60 or 90 minutes, at individual Linux PCs)
8:30 – 10:00	Databases, geometry and proper refinement, Garib Murshudov
10:00 – 10:30	Coffee break
10:30 – 12:00	ArpWarp, Gerrit Langer, Guillaume Evrard
12:00 – 13:45	Lunch (Masarykova kolej)
13:45 – 15:15	Docking, Pingping Guan
15:15 – 15:45	Coffee break
15:45 – 17:15	Coot, Bernhard Lohkamp
17:15	Closing remarks (Jan Dohnálek)