Blind docking of drug-sized compounds to proteins with up to a thousand residues

FEBS Letters

Volumn 580, Issue 5, 2006, Pages 1447-1450

  Hetényi, Csaba ^a   Van Der Spoel, David ^b  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Active site; AutoDock; Binding pocket; Molecular interaction; Pharmacophore; Rational design

Indexed keywords

AMINO ACID;

ARTICLE; BINDING SITE; MOLECULAR INTERACTION; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN TARGETING;

BINDING SITES; COMPUTER SIMULATION; DRUG DELIVERY SYSTEMS; DRUG DESIGN; LIGANDS; METHODS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEINS;

EID: 32344440995     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.01.074     Document Type: Article

References (17)

1. N. Brooijmans, and I.D. Kuntz Molecular recognition and docking algorithms Annu. Rev. Biophys. Biomol. Struct. 32 2003 335 373
2. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662
3. C. Hetényi, and D. van der Spoel Efficient docking of peptides to proteins without prior knowledge of the binding site Protein Sci. 11 2002 1729 1737
4. S.J. Campbell, N.D. Gold, R.M. Jackson, and D.R. Westhead Ligand binding: functional site location, similarity and docking Curr. Opin. Struct. Biol. 13 2003 389 395
5. L. Jining, I. Makagiansar, H. Yusuf-Makagiansar, V.T.K. Chow, T.J. Siahaan, and S.D.S. Jois Design, structure and biological activity of β-turn peptides of CD2 protein for inhibition of T-cell adhesion Eur. J. Biochem. 271 2004 2873 2886
6. W.M. Brown, and D.L. Vander Jagt Creating artificial binding pocket boundaries to improve the efficiency of flexible ligand docking J. Chem. Inf. Comput. Sci. 44 2004 1412 1422
7. O. Pineda, J. Farràs, L. Maccari, F. Manetti, M. Botta, and J. Vilarrasa Computational comparison of microtubule-stabilising agents laulimalide and peloruside with taxol and colchicine Bioorg. Med. Chem. Lett. 14 2004 4825 4829
8. S. Bjelic, and J. Åqvist Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site Biochemistry 43 2004 14521 14528
9. + channel using docking and molecular dynamics methods FEBS Lett. 579 2005 2939 2944
10. ATP channel J. Gen. Physiol. 126 2005 285 299
11. H. Alonso, M.B. Gillies, P.L. Cummins, A.A. Bliznyuk, and J.E. Gready Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase J. Comput.-Aided Mol. Des. 19 2005 165 187
12. M.J. Yonkunas, Y. Xu, and P. Tang Anesthetic interaction with ketosteroid isomerase: insights from molecular dynamics simulations Biophys. J. 89 2005 2350 2356
13. C. Hetényi, U. Maran, and M. Karelson A comprehensive docking study on the selectivity of binding of aromatic compounds to proteins J. Chem. Inf. Comput. Sci. 43 2003 1576 1583
14. E. Lindahl, and M. Delarue Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization Nucleic Acids Res. 33 2005 4496 4506
15. M. Rarey, B. Kramer, and T. Lengauer The particle concept: placing discrete water molecules during protein-ligand docking predictions Proteins 34 1999 17 28
16. F. Österberg, G.M. Morris, M.F. Sanner, A.J. Olson, and D.S. Goodsell Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock Proteins 46 2002 34 40
17. W.L. DeLano PyMol Molecular Graphics System 2002 DeLano Scientific San Carlos, CA, USA