Nothing is for free in this world, not even our facilities. You can use everything for free, but if you want to help us keeping these facilities up and running, then please cite our work liberally.

The overall reference for these facilities is:
A series of PDB-related databanks for everyday needs
Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, E. Krieger, Robbie P. Joosten and Gert Vriend.
Nucl. Acids Res. first published online October 28, 2014. doi:10.1093/nar/gku1028. PDF.


WHAT IF: A molecular modeling and drug design program.
G.Vriend, J. Mol. Graph. (1990) 8, 52-56.


Errors in protein structures.
R.W.W. Hooft, G. Vriend, C. Sander, E.E. Abola, Nature (1996) 381, 272-272.

Who checks the checkers? Four validation tools applied to eight atomic resolution structures.
KS Wilson, S Butterworth, Z Dauter, VS Lamzin, M Walsh, S Wodak, J Pontius, J Richelle, A Vaguine, C Sander, RWW Hooft, G Vriend, JM Thornton, RA Laskowski, MW MacArthur, EJ Dodson, G Murshudov, TJ Oldfield, R Kaptein, JAC Rullmann (1998) Journal of Molecular Biology 276, 417-436.

Validation of protein structures derived by NMR spectroscopy.
Chris AEM Spronk, Sander B Nabuurs, Elmar Krieger, Gert Vriend, Geerten W Vuister (2004) Progress in Nuclear Magnetic Resonance Spectroscopy 45, 315-337.


Errors in protein structures.
R.W.W. Hooft, G. Vriend, C. Sander, E.E. Abola, Nature (1996) 381, 272-272.

WHAT IF web servers

Homology modelling and spectroscopy, a never-ending love story.
Hanka Venselaar, Robbie P. Joosten, Bas Vroling, Coos A. B. Baakman, Maarten L. Hekkelman, Elmar Krieger and Gert Vriend. EBJ 2010 39, 551-563.

WHAT IF web services

WIWS: a protein structure bioinformatics Web service collection.
M.L.Hekkelman, T.A.Te Beek, S.R. Pettifer, D. Thorne, T.K. Attwood, G. Vriend NAR (2010) 38, W719-723.


Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.
RP Joosten, T Womack, G Vriend, G Bricogne Acta Crystallographica Section D: Biological Crystallography 65 (2), 176-185.
PDB_REDO: automated re-refinement of X-ray structure models in the PDB
R. P. Joosten, J. Salzemann, V. Bloch, H. Stockinger, A.-C. Berglund, C. Blanchet, E. Bongcam-Rudloff, C. Combet, A. L. Da Costa, G. Deleage, M. Diarena, R. Fabbretti, G. Fettahi, V. Flegel, A. Gisel, V. Kasam, T. Kervinen, E. Korpelainen, K. Mattila, M. Pagni, M. Reichstadt, V. Breton, I. J. Tickle, G. Vriend. J. Appl. Cryst. (2009). 42, 376-384.
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank
Robbie P. Joosten1, Krista Joosten1, Serge X. Cohen, Gert Vriend, Anastassis Perrakis, Bioinformatics (2011) 27, 3392-3398.


BDB: Databank of PDB files with consistent B-factors
Wouter G. Touw, Gert Vriend (2014) Protein Engineering, Design and Selection (PEDS) 27(11): 457-462. doi: 10.1093/protein/gzu044.


Please use the WHAT IF reference and the general reference for the Lists.


Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Kabsch W, Sander C, Biopolymers. (1983) 22 2577-2637. But as we rewrote the software twice, please cite the general reference too.


The original reference is:
Database of homology derived protein structures and the structural meaning of sequence alignment.
Chris Sander and Reinhard Schneider. Proteins, 9, 56-69, (1991).
But as we rewrote the software twice, please cite the general reference too.


Negative results are hard to publish :-)
Please use the general reference for WHY_NOT.


The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value.
R.W.W. Hooft, C. Sander and G. Vriend., CABIOS (1996) 12, 525-529. (CABIOS is called Bioinformatics these days)


Verification of protein structures: Side-chain planarity.
R.W.W. Hooft, C.Sander and G.Vriend, J. Appl. Cryst. (1996) 29, 714-716. (This seems strange but this is indeed the article in which PDB_SELECT was described.


MRS: A fast and compact retrieval system for biological data.
Hekkelman M.L., Vriend G. Nucleic Acids Research 2005 33(Web Server issue):W766-W769.