Introduction

The protein verification tools from the WHAT IF program are available as a free stand-alone program, complete with all source code. Please look at the documentation that is available for the WHAT_CHECK output.

Conditions

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:

  1. You cannot redistribute without our explicit permission to do so.
  2. If you modify the program (or datafiles, etc), you have to make that new code available to us.
  3. You make the proper acknowledgements, and/or refer to the proper articles.
  4. You cannot sell WHAT_CHECK or WHAT_CHECK results.
  5. You cannot make WHAT_CHECK based servers or services.

So, WHAT_CHECK is for your 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.

References

WHAT_CHECK. This is the "official" WHAT_CHECK reference
Errors in protein structures.
R.W.W. Hooft, G. Vriend, C. Sander, E.E. Abola, Nature (1996) 381, 272-272.
 
DSSP. DSSP determines secondary structures. You need a special license for using DSSP. WHAT_CHECK works slightly worse in a few options if you don't have DSSP available.
Dictionary of protein secondary structure: pattern recognition of hydrogen bond and geometrical features.
W.Kabsch and C.Sander, Biopolymers 22, 2577--2637 (1983).
 
WHAT IF. This is the official WHAT IF reference. WHAT IF is by now the mother of all molecular software packages....
WHAT IF: a molecular modelling and drug design program.
G. Vriend, J. Mol. Graph. 8 52--56 (1990).
 
Bond lengths and angles.
Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement.
R.Engh and R.Huber, Acta Cryst. A47, 392--400 (1991).
 
New parameters for the refinement of nucleic acid-containing structures.
Parkinson, G.; Voitechovsky, J.; Clowney, L.; Brünger, A.T.; Berman, H. Acta Cryst. D52, 57--64 (1996).
 
Matthews Coefficient.
Solvent Content of Protein Crystals
B.W. Matthews J. Mol. Biol. 33, 491--497 (1968).
 
Puckering parameters.
A general definition of ring puckering coordinates
D.Cremer and J.A.Pople, J. Am. Chem. Soc. 97, 1354--1358 (1975).
 
Quality Control for directional atomic contact analysis.
Quality control of protein models: directional atomic contact analysis.
G.Vriend and C.Sander, J. Appl. Cryst. 26, 47--60 (1993).
 
Symmetry Checks.
Reconstruction of symmetry related molecules from protein data bank (PDB) files.
R.W.W.Hooft, C.Sander and G.Vriend, J. Appl. Cryst. 27, 1006--1009 (1994).
 
Hydrogen bond networks and His, Asn, and Gln flips.
Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures.
R.W.W.Hooft, C.Sander and G.Vriend, PROTEINS (1996) 26, 363-376.