Flexible protein-ligand docking using the fleksy protocol

Journal of Computational Chemistry

Volumn 33, Issue 12, 2012, Pages 1215-1217

  Wagener, Markus ^a,b   Ve Vlieg, Jacob ^a,c   Nabuurs, Sander B ^c,d  

^a MSD   (Netherlands)

^b RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^c GRÜNENTHAL GMBH   (Germany)

^d Lead Pharma Medicine BV   (Netherlands)

Author keywords

Docking; Induced fit; Ligand; Modeling; Protein

Indexed keywords

BENCHMARK DATASETS; CROSSDOCKING; DOCKING PROCESS; FLEXIBLE DOCKING; INDUCED FIT; PROTEIN FLEXIBILITY; PROTEIN-LIGAND COMPLEXES; PROTEIN-LIGAND DOCKING; THREE DIMENSIONAL GEOMETRY;

BENCHMARKING; COMPLEXATION; DOCKING; LIGANDS; MODELS;

PROTEINS;

LIGAND; PROTEIN;

CHEMISTRY; COMPUTER PROGRAM; MOLECULAR DOCKING; PROCEDURES;

LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEINS; SOFTWARE;

EID: 84860835824     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.22948     Document Type: Article

References (13)

1. S. B. Nabuurs, M. Wagener, J. de Vlieg, J. Med. Chem. 2007, 50, 6507.
2. J. Gasteiger, C. Rudolph, J. Sadowski, Tetrahedron Comput. Methodol. 1990, 3, 537.
3. A. A. Canutescu, A. A. Shelenkov, R. L. Dunbrack, Jr., Prot. Sci. 2003, 12, 2001.
4. H. Claussen, C. Buning, M. Rarey, T. Lengauer, J. Mol. Biol. 2001, 308, 377.
5. T. Polgar, G. M. Keseru, J. Chem. Inf. Model. 2006, 46, 1795.
6. E. Krieger, K. Joo, J. Lee, S. Raman, J. Thompson, M. Tyka, D. Baker, K. Karplus, Proteins 2009, 77(Suppl 9),114.
7. L. Roumen, M. P. A. Sanders, B. Vroling, I. J. P. de Esch, J. de Vlieg, R. Leurs, J. P. G. Klomp, S. B. Nabuurs, C. de Graaf, Pharmaceuticals 2011, 4, 1196.
8. I. Kufareva, M. Rueda, V. Katritch, R. C. Stevens, R. Abagyan, Structure 2011, 19, 1108.
9. M. Rarey, B. Kramer, T. Lengauer, G. Klebe, J. Mol. Biol. 1996, 261, 470.
10. M. L. Verdonk, P. N. Mortenson, R. J. Hall, M. J. Hartshorn, C. W. Murray, J. Chem. Inf. Model. 2008, 48, 2214.
11. J. S. Duca, V. S. Madison, J. H. Voigt, J. Chem. Inf. Model. 2008, 48, 659.
12. J. H. Voigt, C. Elkin, V. S. Madison, J. S. Duca, J. Chem. Inf. Model. 2008, 48, 669.
13. T. O. Fischmann, A. Hruza, J. S. Duca, L. Ramanathan, T. Mayhood, W. T. Windsor, H. V. Le, T. J. Guzi, M. P. Dwyer, K. Paruch, R. J. Doll, E. Lees, D. Parry, W. Seghezzi, V. Madison, Biopolymers 2008, 89, 372.