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Volumn 7, Issue 3, 2010, Pages

In silico docking and scoring of fragments

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTAMASE INHIBITOR; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE INHIBITOR; PROTEIN;

EID: 78650717723     PISSN: 17406749     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ddtec.2010.11.002     Document Type: Review
Times cited : (19)

References (46)
  • 1
    • 46849089254 scopus 로고    scopus 로고
    • Recent developments in fragment-based drug discovery
    • M. Congreve Recent developments in fragment-based drug discovery J. Med. Chem. 51 2008 3661 3680
    • (2008) J. Med. Chem. , vol.51 , pp. 3661-3680
    • Congreve, M.1
  • 2
    • 0141726877 scopus 로고    scopus 로고
    • A 'rule of three' for fragment-based lead discovery?
    • M. Congreve A 'rule of three' for fragment-based lead discovery? Drug Discov. Today 8 2003 876 877
    • (2003) Drug Discov. Today , vol.8 , pp. 876-877
    • Congreve, M.1
  • 3
    • 16244388286 scopus 로고    scopus 로고
    • Virtual exploration of the small-molecule chemical universe below 160 Daltons
    • T. Fink Virtual exploration of the small-molecule chemical universe below 160 Daltons Angew. Chem. Int. Ed. Engl. 44 2005 1504 1508
    • (2005) Angew. Chem. Int. Ed. Engl. , vol.44 , pp. 1504-1508
    • Fink, T.1
  • 4
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • J.J. Irwin, and B.K. Shoichet ZINC - a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 5
    • 56749182336 scopus 로고    scopus 로고
    • Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors
    • J.W. Huang Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors J. Med. Chem. 51 2008 7111 7118
    • (2008) J. Med. Chem. , vol.51 , pp. 7111-7118
    • Huang, J.W.1
  • 6
    • 33745199815 scopus 로고    scopus 로고
    • Virtual ligand screening: Strategies, perspectives and limitations
    • G. Klebe Virtual ligand screening: strategies, perspectives and limitations Drug Discov. Today 11 2006 580 594
    • (2006) Drug Discov. Today , vol.11 , pp. 580-594
    • Klebe, G.1
  • 7
    • 34249094150 scopus 로고    scopus 로고
    • Informatics and modeling challenges in fragment-based drug discovery
    • R.E. Hubbard Informatics and modeling challenges in fragment-based drug discovery Curr. Opin. Drug Discov. Dev. 10 2007 289 297
    • (2007) Curr. Opin. Drug Discov. Dev. , vol.10 , pp. 289-297
    • Hubbard, R.E.1
  • 8
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • A. Miranker, and M. Karplus Functionality maps of binding sites: a multiple copy simultaneous search method Proteins 11 1991 29 34
    • (1991) Proteins , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 9
    • 78650734429 scopus 로고    scopus 로고
    • Fragment-docking to proteins with the Multi-copy Simultaneous Search Methodology
    • M.C. Stultz, and M. Karplus Fragment-docking to proteins with the Multi-copy Simultaneous Search Methodology W. Jahnke, D.A. Erlanson, Fragment-based Approaches in Drug Discovery 2006 Wiley-VCH 125 144
    • (2006) Fragment-based Approaches in Drug Discovery , pp. 125-144
    • Stultz, M.C.1    Karplus, M.2
  • 10
    • 33947658802 scopus 로고    scopus 로고
    • Identification of hot spots within druggable binding regions by computational solvent mapping of proteins
    • M.R. Landon Identification of hot spots within druggable binding regions by computational solvent mapping of proteins J. Med. Chem. 50 2007 1231 1240
    • (2007) J. Med. Chem. , vol.50 , pp. 1231-1240
    • Landon, M.R.1
  • 11
    • 68249132213 scopus 로고    scopus 로고
    • Computational fragment-based binding site identification by ligand competitive saturation
    • O. Guvench, and A.D. MacKerell Jr Computational fragment-based binding site identification by ligand competitive saturation PLoS Comput. Biol. 5 2009 e1000435
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000435
    • Guvench, O.1    MacKerell, Jr.A.D.2
  • 12
    • 33244470695 scopus 로고    scopus 로고
    • Grand canonical Monte Carlo simulation of ligand-protein binding
    • M. Clark Grand canonical Monte Carlo simulation of ligand-protein binding J. Chem. Inf. Model. 46 2006 231 242
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 231-242
    • Clark, M.1
  • 13
    • 68149095775 scopus 로고    scopus 로고
    • Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics
    • D. Ekonomiuk Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics J. Med. Chem. 52 2009 4860 4868
    • (2009) J. Med. Chem. , vol.52 , pp. 4860-4868
    • Ekonomiuk, D.1
  • 14
    • 67651002876 scopus 로고    scopus 로고
    • Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
    • K. Loving Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation J. Comput. Aided Mol. Des. 2009
    • (2009) J. Comput. Aided Mol. Des.
    • Loving, K.1
  • 15
    • 33947612966 scopus 로고    scopus 로고
    • Application of fragment screening by X-ray crystallography to beta-secretase
    • C.W. Murray Application of fragment screening by X-ray crystallography to beta-secretase J. Med. Chem. 50 2007 1116 1123
    • (2007) J. Med. Chem. , vol.50 , pp. 1116-1123
    • Murray, C.W.1
  • 16
    • 37849043411 scopus 로고    scopus 로고
    • Application of fragment-based lead generation to the discovery of novel, cyclic amidine beta-secretase inhibitors with nanomolar potency, cellular activity, and high ligand efficiency
    • P.D. Edwards Application of fragment-based lead generation to the discovery of novel, cyclic amidine beta-secretase inhibitors with nanomolar potency, cellular activity, and high ligand efficiency J. Med. Chem. 50 2007 5912 5925
    • (2007) J. Med. Chem. , vol.50 , pp. 5912-5925
    • Edwards, P.D.1
  • 17
    • 66149158600 scopus 로고    scopus 로고
    • Docking for fragment inhibitors of AmpC beta-lactamase
    • D.G. Teotico Docking for fragment inhibitors of AmpC beta-lactamase Proc. Natl. Acad. Sci. U. S. A. 106 2009 7455 7460
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 7455-7460
    • Teotico, D.G.1
  • 18
    • 65349195698 scopus 로고    scopus 로고
    • Molecular docking and ligand specificity in fragment-based inhibitor discovery
    • Y. Chen, and B.K. Shoichet Molecular docking and ligand specificity in fragment-based inhibitor discovery Nat. Chem. Biol. 5 2009 358 364
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 358-364
    • Chen, Y.1    Shoichet, B.K.2
  • 19
    • 31344459599 scopus 로고    scopus 로고
    • In silico fragment-based discovery of DPP-IV S1 pocket binders
    • C. Rummey In silico fragment-based discovery of DPP-IV S1 pocket binders Bioorg. Med. Chem. Lett. 16 2006 1405 1409
    • (2006) Bioorg. Med. Chem. Lett. , vol.16 , pp. 1405-1409
    • Rummey, C.1
  • 20
    • 24944529911 scopus 로고    scopus 로고
    • Virtual screening against metalloenzymes for inhibitors and substrates
    • J.J. Irwin Virtual screening against metalloenzymes for inhibitors and substrates Biochemistry 44 2005 12316 12328
    • (2005) Biochemistry , vol.44 , pp. 12316-12328
    • Irwin, J.J.1
  • 21
    • 67650754042 scopus 로고    scopus 로고
    • One scaffold, three binding modes: Novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening
    • C.P. Mpamhanga One scaffold, three binding modes: novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening J. Med. Chem. 52 2009 4454 4465
    • (2009) J. Med. Chem. , vol.52 , pp. 4454-4465
    • Mpamhanga, C.P.1
  • 22
    • 77955330853 scopus 로고    scopus 로고
    • Virtual fragment screening for novel inhibitors of 6-phosphogluconate dehydrogenase
    • G.F. Ruda Virtual fragment screening for novel inhibitors of 6-phosphogluconate dehydrogenase Bioorg. Med. Chem. 18 2010 5056 5062
    • (2010) Bioorg. Med. Chem. , vol.18 , pp. 5056-5062
    • Ruda, G.F.1
  • 23
    • 41849136839 scopus 로고    scopus 로고
    • Novel prostaglandin D synthase inhibitors generated by fragment-based drug design
    • M. Hohwy Novel prostaglandin D synthase inhibitors generated by fragment-based drug design J. Med. Chem. 51 2008 2178 2186
    • (2008) J. Med. Chem. , vol.51 , pp. 2178-2186
    • Hohwy, M.1
  • 24
    • 67650997041 scopus 로고    scopus 로고
    • Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide
    • S. Kawatkar Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide J. Comput. Aided Mol. Des. 2009
    • (2009) J. Comput. Aided Mol. Des.
    • Kawatkar, S.1
  • 25
    • 36248956723 scopus 로고    scopus 로고
    • The SeeDs approach: Integrating fragments into drug discovery
    • R.E. Hubbard The SeeDs approach: integrating fragments into drug discovery Curr. Top. Med. Chem. 7 2007 1568 1581
    • (2007) Curr. Top. Med. Chem. , vol.7 , pp. 1568-1581
    • Hubbard, R.E.1
  • 26
    • 77954036921 scopus 로고    scopus 로고
    • Virtual fragment docking by Glide: A validation study on 190 protein-fragment complexes
    • M. Sandor Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes J. Chem. Inf. Model 50 2010 1165 1172
    • (2010) J. Chem. Inf. Model , vol.50 , pp. 1165-1172
    • Sandor, M.1
  • 27
    • 67650951150 scopus 로고    scopus 로고
    • The multiple roles of computational chemistry in fragment-based drug design
    • R. Law The multiple roles of computational chemistry in fragment-based drug design J. Comput. Aided Mol. Des. 23 2009 459 473
    • (2009) J. Comput. Aided Mol. Des. , vol.23 , pp. 459-473
    • Law, R.1
  • 28
    • 49649114644 scopus 로고    scopus 로고
    • Fragment docking to S100 proteins reveals a wide diversity of weak interaction sites
    • Y. Arendt Fragment docking to S100 proteins reveals a wide diversity of weak interaction sites ChemMedChem 2 2007 1648 1654
    • (2007) ChemMedChem , vol.2 , pp. 1648-1654
    • Arendt, Y.1
  • 29
    • 76649089979 scopus 로고    scopus 로고
    • Library screening by fragment-based docking
    • D. Huang, and A. Caflisch Library screening by fragment-based docking J. Mol.Recognit. 23 2009 183 193
    • (2009) J. Mol.Recognit. , vol.23 , pp. 183-193
    • Huang, D.1    Caflisch, A.2
  • 30
    • 69549135452 scopus 로고    scopus 로고
    • Fragment-based computation of binding free energies by systematic sampling
    • M. Clark Fragment-based computation of binding free energies by systematic sampling J. Chem. Inf. Model. 49 2009 1901 1913
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1901-1913
    • Clark, M.1
  • 31
    • 52249108519 scopus 로고    scopus 로고
    • CONFIRM: Connecting fragments found in receptor molecules
    • D.C. Thompson CONFIRM: connecting fragments found in receptor molecules J. Comput. Aided Mol. Des. 22 2008 761 772
    • (2008) J. Comput. Aided Mol. Des. , vol.22 , pp. 761-772
    • Thompson, D.C.1
  • 32
    • 33748652464 scopus 로고    scopus 로고
    • FlexNovo: Structure-based searching in large fragment spaces
    • J. Degen, and M. Rarey FlexNovo: structure-based searching in large fragment spaces ChemMedChem 1 2006 854 868
    • (2006) ChemMedChem , vol.1 , pp. 854-868
    • Degen, J.1    Rarey, M.2
  • 33
    • 23844449940 scopus 로고    scopus 로고
    • Computer-based de novo design of drug-like molecules
    • G. Schneider, and U. Fechner Computer-based de novo design of drug-like molecules Nat. Rev. Drug Discov. 4 2005 649 663
    • (2005) Nat. Rev. Drug Discov. , vol.4 , pp. 649-663
    • Schneider, G.1    Fechner, U.2
  • 34
    • 77949345618 scopus 로고    scopus 로고
    • Computational approaches for fragment-based and de novo design
    • K. Loving Computational approaches for fragment-based and de novo design Curr. Top. Med. Chem. 10 2010 14 32
    • (2010) Curr. Top. Med. Chem. , vol.10 , pp. 14-32
    • Loving, K.1
  • 35
    • 0041989635 scopus 로고    scopus 로고
    • Conformational flexibility models for the receptor in structure based drug design
    • M.L. Teodoro, and L.E. Kavraki Conformational flexibility models for the receptor in structure based drug design Curr. Pharm. Des. 9 2003 1635 1648
    • (2003) Curr. Pharm. Des. , vol.9 , pp. 1635-1648
    • Teodoro, M.L.1    Kavraki, L.E.2
  • 36
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • H.A. Carlson, and J.A. McCammon Accommodating protein flexibility in computational drug design Mol. Pharmacol. 57 2000 213 218
    • (2000) Mol. Pharmacol. , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 37
    • 1842471241 scopus 로고    scopus 로고
    • Testing a flexible-receptor docking algorithm in a model binding site
    • B.Q. Wei Testing a flexible-receptor docking algorithm in a model binding site J. Mol. Biol. 337 2004 1161 1182
    • (2004) J. Mol. Biol. , vol.337 , pp. 1161-1182
    • Wei, B.Q.1
  • 38
    • 52049093435 scopus 로고    scopus 로고
    • A poke in the eye: Inhibiting HIV-1 protease through its flap-recognition pocket
    • K.L. Damm A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket Biopolymers 89 2008 643 652
    • (2008) Biopolymers , vol.89 , pp. 643-652
    • Damm, K.L.1
  • 39
    • 40649101151 scopus 로고    scopus 로고
    • Rescoring docking hit lists for model cavity sites: Predictions and experimental testing
    • A.P. Graves Rescoring docking hit lists for model cavity sites: predictions and experimental testing J. Mol. Biol. 377 2008 914 934
    • (2008) J. Mol. Biol. , vol.377 , pp. 914-934
    • Graves, A.P.1
  • 40
    • 50249094315 scopus 로고    scopus 로고
    • Exploiting ordered waters in molecular docking
    • N. Huang, and B.K. Shoichet Exploiting ordered waters in molecular docking J. Med. Chem. 51 2008 4862 4865
    • (2008) J. Med. Chem. , vol.51 , pp. 4862-4865
    • Huang, N.1    Shoichet, B.K.2
  • 41
    • 0035044857 scopus 로고    scopus 로고
    • Experimental and computational mapping of the binding surface of a crystalline protein
    • A.C. English Experimental and computational mapping of the binding surface of a crystalline protein Protein Eng. 14 2001 47 59
    • (2001) Protein Eng. , vol.14 , pp. 47-59
    • English, A.C.1
  • 42
    • 33749242759 scopus 로고    scopus 로고
    • Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
    • J. Tirado-Rives, and W.L. Jorgensen Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding J. Med. Chem. 49 2006 5880 5884
    • (2006) J. Med. Chem. , vol.49 , pp. 5880-5884
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 43
    • 67650149263 scopus 로고    scopus 로고
    • QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors
    • M.P. Gleeson, and D. Gleeson QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors J. Chem. Inf. Model. 49 2009 1437 1448
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1437-1448
    • Gleeson, M.P.1    Gleeson, D.2
  • 44
    • 33846933784 scopus 로고    scopus 로고
    • Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
    • G. Marcou, and D. Rognan Optimizing fragment and scaffold docking by use of molecular interaction fingerprints J. Chem. Inf. Model. 47 2007 195 207
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 195-207
    • Marcou, G.1    Rognan, D.2
  • 45
    • 68149170106 scopus 로고    scopus 로고
    • Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring
    • R. Friedman, and A. Caflisch Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring ChemMedChem 4 2009 1317 1326
    • (2009) ChemMedChem , vol.4 , pp. 1317-1326
    • Friedman, R.1    Caflisch, A.2
  • 46
    • 70449522914 scopus 로고    scopus 로고
    • Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
    • S.E. Boyce Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site J. Mol. Biol. 394 2009 747 763
    • (2009) J. Mol. Biol. , vol.394 , pp. 747-763
    • Boyce, S.E.1


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