Presenters

	Robbie Joosten recently completed his PhD at the CMBI with as topic "Protein Structure Validation". His PhD project consisted of two major topics. The first topic was the detection of errors in PDB files. The second topic was rerefinement of all X-ray PDB files. After obtaining his PhD, Robbie moved to the X-ray department of the Dutch cancer institute (the NKI in Amsterdam) where he continues with the further improvement of (all) X-ray PDB files.
	Jurgen Doreleijers got his PhD in the group of Rob Kapteyn in Utrecht with as topic NMR protein structure quality. After his PhD defense Jurgen moved to the BMRB in Wisconsin, USA. Here he worked on the remediation of the experimental NMR data that has been deposited with the NMR structure ensembles in the PDB. Jurgen recently moved to the CMBI where he works in the group of Geerten Vuister on the CING software that evaluates NMR structures.
	Hanka Venselaar is a PhD student at the CMBI. Her research project (automation of the prediction of the phenotypic effects of protein point mutations). This project includes extensive studies of protein structures and often involves a multitude of protein structure quality aspects.
	Gert Vriend is one of the pioneers in the field of protein structure quality determination. His WHAT_CHECK software is for many years already the de facto standard in this field. He has published dozens of articles in this field, and he has been the PhD supervisor of a series of PhD students who worked on the structure validation of X-ray or NMR files.

Motivation

Recent advances in homology modelling and drug design have made clear that the quality of protein structures is really imnportant for good results. Today's software and CPU time availability on clusters, super computers, and the grid allow for easy improvement of old files. It is therefore important for all protein structure bioinformaticians to be able to evaluate the quality of the structures used in their studies and to know when it might be beneficial to ask an NMR spectroscopist or X-ray crystallographer to help bring an old file up to today's standards.

Goals

This workshop will teach the participants how to use a series of protein structure validation tools and how to interpret the results. The origins of problems are discussed as well as their importance for follow up studies.

Prerequisites

In silico experience with protein structures is required. We will assume that the participants of this workshop have spent at least a hundred hours studying protein structures with molecular visualisation software. Extensive knowledge of any particular visualisation program, however, is not required.
Candidates who cannot bring their own portable computer are requested to contact the organisers as only a limited number of loan-PCs is available.

Tutorial outline

Seminars

Gert Vriend - Introduction
Robbie Joosten - X-ray structure evaluation
Jurgen Doreleijers - NMR structure evaluation

Practicals

Hanka venselaar - Using the YASARA twinset for protein structure evaluation
Gert Vriend - Reading WHAT_CHECK reports

Parallel sessions:
Jurgen Doreleijers - Using CING to evaluate protein structures
Robbie Joosten - Errors in X-ray structures