WhatCheck has been derived from a subset of protein verification tools from the WHATIF program, this does extensive checking of many sterochemical parameters of the residues in the model.

The final homology model has to be evaluated to make sure that the structural features of the model are consistent with the physicochemical rules. This involves checking anomalies in φ–ψ angles, bond lengths, close contacts, and so on. Another way of checking the quality of a protein model is to implicitly take these stereochemical properties into account. This is a method that detects errors by compiling statistical profiles of spatial features and interaction energy from experimentally determined structures. By comparing the statistical parameters with the constructed model, the method reveals which regions of a sequence appear to be folded normally and which regions do not. If structural irregularities are found, the region is considered to have errors and has to be further refined.

Homology modeling is rapidly becoming the method of choice for obtaining three-dimensional coordinates for proteins because genome projects produce sequences at a much higher rate than NMR and X-ray laboratories can solve the three-dimensional structures. The quality of protein models will not be immediately clear to novices and support with the evaluation seems to be needed. Expert users are sometimes interested in evaluating the quality of modeling programs rather than the quality of the models themselves.

WHATCHECK is a program that can be used to detect deviations in protein structures, specifically for large-scale studies. It can be run through a web application or as a standalone software and does not need experimental data. The software has been tested on more than 3000 structures from the Brookhaven Protein Data Bank.

It is a comprehensive protein analysis server that validates a protein model for chemical correctness. It has many functions, including checking of planarity, collisions with symmetry axes (closecontacts), proline puckering, anomalous bond angles, and bond lengths. It also allows the generation of Ramachandran plots as an assessment of the quality of the model.

Commercial and non-commercial users are free to download WHAT_CHECK, and use it for all forms of research and education. However, there are some restrictions. As WHAT_CHECK now is totally ′open′ these are not hard conditions, but we would appreciate if people would bound to these rules anyway:

• We cannot redistribute without our explicit permission to do so.

• If we modify the program (or data-files, etc), we have to make that new code available to us.

• We make the proper acknowledgements, and/or refer to the proper articles.

• We cannot make WHAT_CHECK based servers or services.

• You can neither sell WHAT_CHECK stand-alone, nor as part of other software.

So, WHAT_CHECK is for our research/education purposes only. Of course, industry can sell all products produced using WHAT_CHECK without restrictions, but nobody can start selling WHAT_CHECK reports, and nobody is allowed to make a WWW server that produces WHAT_CHECK results or modified WHAT_CHECK results for predicted protein models.