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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. |
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The overall reference for these facilities is: |
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.
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.
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.