http://publicationslist.org/data/w.mooij/atom.xmlWijnand Mooij's Publications List Wijnand Mooijhttp://publicationslist.org/w.mooij$basepathfavicon.icoRecent additions to Wijnand Mooij's PublicationsList.org pagehttp://publicationslist.org/publications.png2010-07-28T07:43:47Z http://publicationslist.org/w.mooij/refid3 2010-07-26T20:42:09Z "Conditional Restraints": Restraining the Free Atoms in ARP/wARP. The automated building of a protein model into an electron density map remains a challenging problem. In the ARP/wARP approach, model building is facilitated by initially interpreting a density map with free atoms of unknown chemical identity; all structural information for such chemically unassigned atoms is discarded. Here, this is remedied by applying restraints between free atoms, and between ...<br/><br/>Wijnand T M Mooij, Serge X Cohen, Krista Joosten, Garib N Murshudov, Anastassis Perrakis (2009) <i>Structure</i> <i></i> <i></i> 17: 183-189<br/> http://publicationslist.org/w.mooij/refid2 2010-07-28T07:43:24Z ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiments. ProteinCCD (CCD for Crystallographic Construct Design) aims to facilitate a common practice in structural biology, namely the design of several truncation constructs of the protein under investigation, based on experimental data or on sequence analysis tools. ProteinCCD functions as a meta-server, available online at http://xtal.nki.nl/ccd, that collects information from prediction servers concern...<br/><br/>Wijnand T M Mooij, Eirini Mitsiki, Anastassis Perrakis (2009) <i>Nucleic Acids Res</i> <i></i> <i></i> : Web Server issue W402-W405<br/> http://publicationslist.org/w.mooij/refid13 2010-07-27T10:35:08Z Knowledge-Based Methods in Structure-Based Design Marcel L. Verdonk and Wijnand T. M. Mooij (2008) <i>Computational and Structural Approaches to Drug Discovery: Ligand-Protein Interactions</i> 111-126<br/> http://publicationslist.org/w.mooij/refid11 2010-07-27T11:13:28Z A knowledge-driven approach for crystallographic protein model completion Krista Joosten, Serge X. Cohen, Paul Emsley, Wijnand T.M. Mooij, Victor S Lamzin (2008) <i>Acta Crystallogr</i> D64: 416-424<br/> http://publicationslist.org/w.mooij/refid4 2010-07-28T07:43:40Z Diverse, high-quality test set for the validation of protein-ligand docking performance. A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do no...<br/><br/>Michael J Hartshorn, Marcel L Verdonk, Gianni Chessari, Suzanne C Brewerton, Wijnand T M Mooij, Paul N Mortenson, Christopher W Murray (2007) <i>J Med Chem</i> <i></i> <i></i> 50: 726-741<br/> http://publicationslist.org/w.mooij/refid5 2010-07-28T07:43:00Z Automated protein-ligand crystallography for structure-based drug design. An approach to automate protein-ligand crystallography is presented, with the aim of increasing the number of structures available to structure-based drug design. The methods we propose deal with the automatic interpretation of diffraction data for targets with known protein structures, and provide easy access to the results. Central to the system is a novel procedure that fully automates the plac...<br/><br/>Wijnand T M Mooij, Michael J Hartshorn, Ian J Tickle, Andrew J Sharff, Marcel L Verdonk, Harren Jhoti (2006) <i>ChemMedChem</i> <i></i> <i></i> 1: 827-838<br/> http://publicationslist.org/w.mooij/refid6 2010-07-27T11:08:05Z General and targeted statistical potentials for protein-ligand interactions. We present a novel atom-atom potential derived from a database of protein-ligand complexes. First, we clarify the similarities and differences between two statistical potentials described in the literature, PMF and Drugscore. We highlight shortcomings caused by an important factor unaccounted for in their reference states, and describe a new potential, which we name the Astex Statistical Potential...<br/><br/>Wijnand T M Mooij, Marcel L Verdonk (2005) <i>Proteins: Struct Funct and Bioinf</i> <i></i> <i></i> 61: 272-287<br/> http://publicationslist.org/w.mooij/refid7 2010-07-26T20:41:04Z Virtual screening using protein-ligand docking: avoiding artificial enrichment. This study addresses a number of topical issues around the use of protein-ligand docking in virtual screening. We show that, for the validation of such methods, it is key to use focused libraries (containing compounds with one-dimensional properties, similar to the actives), rather than "random" or "drug-like" libraries to test the actives against. We also show that, to obtain good enrichments, th...<br/><br/>Marcel L Verdonk, Valerio Berdini, Michael J Hartshorn, Wijnand T M Mooij, Christopher W Murray, Richard D Taylor, Paul Watson (2004) <i>J Chem Inf Comput Sci</i> <i></i> <i></i> 44: 793-806<br/> http://publicationslist.org/w.mooij/refid12 2010-07-27T10:58:29Z Testing the Quality of Some Recent Water-Water Potentials Jeanne G. C. M. van Duijneveldt-van de Rijdt, Wijnand T. M. Mooij, Frans B. van Duijneveldt (2003) <i>Phys Chem Chem Phys</i> 5: 1169-1180<br/> http://publicationslist.org/w.mooij/refid8 2010-07-27T10:26:30Z Crystal structure prediction of small organic molecules: a second blind test. The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were us...<br/><br/>W D S Motherwell, H L Ammon, J D Dunitz, A Dzyabchenko, P Erk, A Gavezzotti, D W M Hofmann, F J J Leusen, J P M Lommerse, W T M Mooij, S L Price, H Scheraga, B Schweizer, M U Schmidt, B P van Eijck, P Verwer, D E Williams (2002) <i>Acta Crystallogr</i> <i></i> <i></i> B58: 647-661<br/> http://publicationslist.org/w.mooij/refid20 2010-07-27T11:05:08Z Multipoles versus charges in the 1999 crystal structure prediction test Wijnand T. M. Mooij and Frank J. J. Leusen (2001) <i>Phys Chem Chem Phys</i> 3: 5063-5066<br/> http://publicationslist.org/w.mooij/refid19 2010-07-27T11:06:06Z Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part II. Accurate energy minimization Bouke P. van Eijck, Wijnand T. M. Mooij, Jan Kroon (2001) <i>J Comp Chem</i> 22: 805-815<br/> http://publicationslist.org/w.mooij/refid16 2010-07-27T11:03:31Z Crystal Structure Prediction for Six Monosaccharides Revisited Bouke P. van Eijck, Wijnand T. M. Mooij, and Jan Kroon (2001) <i>J Phys Chem B</i> 105: 10573–10578<br/> http://publicationslist.org/w.mooij/refid9 2010-07-27T12:53:38Z A test of crystal structure prediction of small organic molecules. A collaborative workshop was held in May 1999 at the Cambridge Crystallographic Data Centre to test how well currently available methods of crystal structure prediction perform when given only the atomic connectivity for an organic compound. A blind test was conducted on a selection of four compounds and a wide range of methodologies representing, the principal computer programs currently availabl...<br/><br/>J P M Lommerse, W D S Motherwell, H L Ammon, J D Dunitz, A Gavezzotti, D W M Hofmann, F J J Leusen, W T M Mooij, S L Price, B Schweizer, M U Schmidt, B P van Eijck, P Verwer, D E Williams (2000) <i>Acta Crystallogr</i> <i></i> <i></i> B56: 697-714<br/> http://publicationslist.org/w.mooij/refid21 2010-07-28T07:13:54Z Ab Initio Prediction of Crystal Structures Wijnand T. M. Mooij (2000) <br/> http://publicationslist.org/w.mooij/refid14 2010-07-27T11:04:42Z Ab Initio Crystal Structure Predictions for Flexible Hydrogen-Bonded Molecules Wijnand T. M. Mooij, Bouke P. van Eijck, and Jan Kroon (2000) <i>J Am Chem Soc</i> 122: 3500-3505<br/> http://publicationslist.org/w.mooij/refid17 2010-07-27T11:03:45Z Transferable ab Initio Intermolecular Potentials. 1. Derivation from Methanol Dimer and Trimer Calculations Wijnand T. M. Mooij, Frans B. van Duijneveldt, Jeanne G. C. M. van Duijneveldt-van de Rijdt, and Bouke P. van Eijck (1999) <i>J Phys Chem A</i> 103: 9872–9882<br/> http://publicationslist.org/w.mooij/refid15 2010-07-27T11:05:30Z Transferable ab Initio Intermolecular Potentials. 2. Validation and Application to Crystal Structure Prediction Wijnand T. M. Mooij, Bouke P. van Eijck, and Jan Kroon (1999) <i>J Phys Chem A</i> 103: 9883–9890<br/> http://publicationslist.org/w.mooij/refid18 2010-07-27T11:03:11Z Crystal structure predictions for acetic acid Wijnand T. M. Mooij, Bouke P. van Eijck, Sarah L. Price, Paul Verwer, Jan Kroon (1998) <i>J Comp Chem</i> 19: 459-474<br/> http://publicationslist.org/w.mooij/refid10 2010-07-27T10:59:09Z Hypothetical Crystal Structures of Benzene at 0 and 30 kbar ossible crystal structures of benzene were generated without any prior crystallographic information, using a systematic grid search method. Only structures with one molecule in the asymmetric unit were considered. 31 space groups were investigated, and the resulting structures were clustered and checked for stability upon removal of the space-group symmetry. In the enthalpy range 10 kJ mol-1 30 st...<br/><br/>Bouke P. van Eijck, Anthony L. Spek, Wijnand T. M. Mooij and Jan Kroon (1998) <i>Acta Crystallogr</i> B54: 291-299<br/> http://publicationslist.org/w.mooij/refid1 2010-07-27T11:02:56Z Attempted Prediction of the Crystal Structures of Six Monosaccharides Bouke P. van Eijck, Wijnand T. M. Mooij and Jan Kroon (1995) <i>Acta Crystallogr</i> B51: 99-103<br/>