메뉴 건너뛰기




Volumn 102, Issue 1, 2012, Pages 144-151

Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 84855438940     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.11.4008     Document Type: Article
Times cited : (32)

References (33)
  • 1
    • 0036007208 scopus 로고    scopus 로고
    • Virtual screening and fast automated docking methods
    • G. Schneider, and H.J. Böhm Virtual screening and fast automated docking methods Drug Discov. Today 7 2002 64 70
    • (2002) Drug Discov. Today , vol.7 , pp. 64-70
    • Schneider, G.1    Böhm, H.J.2
  • 3
    • 79954520873 scopus 로고    scopus 로고
    • Sc-PDB: A database for identifying variations and multiplicity of "druggable" binding sites in proteins
    • J. Meslamani, D. Rognan, and E. Kellenberger sc-PDB: a database for identifying variations and multiplicity of "druggable" binding sites in proteins Bioinformatics 27 2011 1324 1326
    • (2011) Bioinformatics , vol.27 , pp. 1324-1326
    • Meslamani, J.1    Rognan, D.2    Kellenberger, E.3
  • 4
    • 10044294023 scopus 로고    scopus 로고
    • An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
    • R. Wang, and Y. Lu S. Wang An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes J. Chem. Inf. Comput. Sci. 44 2004 2114 2125
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 2114-2125
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 6
    • 79959243001 scopus 로고    scopus 로고
    • Thermodynamics of ligand binding and efficiency
    • C.H. Reynolds, and M.K. Holloway Thermodynamics of ligand binding and efficiency ACS Med. Chem. Lett. 2 2011 433 437
    • (2011) ACS Med. Chem. Lett. , vol.2 , pp. 433-437
    • Reynolds, C.H.1    Holloway, M.K.2
  • 7
    • 79952181220 scopus 로고    scopus 로고
    • Challenges and advances in computational docking
    • E. Yuriev, M. Agostino, and P.A. Ramsland Challenges and advances in computational docking J. Mol. Recognit. 24 2009 149 164
    • (2009) J. Mol. Recognit. , vol.24 , pp. 149-164
    • Yuriev, E.1    Agostino, M.2    Ramsland, P.A.3
  • 8
    • 56449127496 scopus 로고    scopus 로고
    • Fully automated molecular mechanics based induced fit protein-ligand docking method
    • J. Koska, and V.Z. Spassov C.M. Venkatachalam Fully automated molecular mechanics based induced fit protein-ligand docking method J. Chem. Inf. Model. 48 2008 1965 1973
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1965-1973
    • Koska, J.1    Spassov, V.Z.2    Venkatachalam, C.M.3
  • 9
    • 65249120827 scopus 로고    scopus 로고
    • Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes
    • M. Rueda, G. Bottegoni, and R. Abagyan Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes J. Chem. Inf. Model. 49 2009 716 725
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 716-725
    • Rueda, M.1    Bottegoni, G.2    Abagyan, R.3
  • 10
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    • DOI 10.1021/jm8001197
    • L.S. Cheng, and R.E. Amaro J.A. McCammon Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase J. Med. Chem. 51 2008 3878 3894 (Pubitemid 351956517)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.13 , pp. 3878-3894
    • Cheng, L.S.1    Amaro, R.E.2    Xu, D.3    Li, W.W.4    Arzberger, P.W.5    McCammon, J.A.6
  • 11
    • 72949087796 scopus 로고    scopus 로고
    • Molecular docking screens using comparative models of proteins
    • H. Fan, and J.J. Irwin A. Sali Molecular docking screens using comparative models of proteins J. Chem. Inf. Model. 49 2009 2512 2527
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2512-2527
    • Fan, H.1    Irwin, J.J.2    Sali, A.3
  • 12
    • 33846404143 scopus 로고    scopus 로고
    • Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family
    • DOI 10.1021/jm061073h
    • R. Soliva, and J.L. Gelpí M. Orozco Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family J. Med. Chem. 50 2007 283 293 (Pubitemid 46147709)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.2 , pp. 283-293
    • Soliva, R.1    Gelpi, J.L.2    Almansa, C.3    Virgili, M.4    Orozco, M.5
  • 13
    • 77957237749 scopus 로고    scopus 로고
    • Rapid flexible docking using a stochastic rotamer library of ligands
    • F. Ding, S. Yin, and N.V. Dokholyan Rapid flexible docking using a stochastic rotamer library of ligands J. Chem. Inf. Model. 50 2010 1623 1632
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1623-1632
    • Ding, F.1    Yin, S.2    Dokholyan, N.V.3
  • 14
    • 33750056673 scopus 로고    scopus 로고
    • ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
    • DOI 10.1002/prot.21086
    • J. Meiler, and D. Baker ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility Proteins 65 2006 538 548 (Pubitemid 44583205)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.3 , pp. 538-548
    • Meiler, J.1    Baker, D.2
  • 15
    • 58149094776 scopus 로고    scopus 로고
    • RosettaLigand docking with full ligand and receptor flexibility
    • I.W. Davis, and D. Baker RosettaLigand docking with full ligand and receptor flexibility J. Mol. Biol. 385 2009 381 392
    • (2009) J. Mol. Biol. , vol.385 , pp. 381-392
    • Davis, I.W.1    Baker, D.2
  • 16
    • 0034996721 scopus 로고    scopus 로고
    • Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking
    • DOI 10.1016/S1074-5521(01)00023-0, PII S1074552101000230
    • A.C. Anderson, and R.H. O'Neil R.M. Stroud Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking Chem. Biol. 8 2001 445 457 (Pubitemid 32455899)
    • (2001) Chemistry and Biology , vol.8 , Issue.5 , pp. 445-457
    • Anderson, A.C.1    O'Neil, R.H.2    Surti, T.S.3    Stroud, R.M.4
  • 17
    • 73349093728 scopus 로고    scopus 로고
    • High-performance drug discovery: Computational screening by combining docking and molecular dynamics simulations
    • N. Okimoto, and N. Futatsugi M. Taiji High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations PLOS Comput. Biol. 5 2009 e1000528
    • (2009) PLOS Comput. Biol. , vol.5 , pp. 1000528
    • Okimoto, N.1    Futatsugi, N.2    Taiji, M.3
  • 18
    • 77952844866 scopus 로고    scopus 로고
    • Single-molecule pulling simulations can discern active from inactive enzyme inhibitors
    • F. Colizzi, and R. Perozzo A. Cavalli Single-molecule pulling simulations can discern active from inactive enzyme inhibitors J. Am. Chem. Soc. 132 2010 7361 7371
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 7361-7371
    • Colizzi, F.1    Perozzo, R.2    Cavalli, A.3
  • 20
    • 52049118327 scopus 로고    scopus 로고
    • MedusaScore: An accurate force field-based scoring function for virtual drug screening
    • S. Yin, and L. Biedermannova N.V. Dokholyan MedusaScore: an accurate force field-based scoring function for virtual drug screening J. Chem. Inf. Model. 48 2008 1656 1662
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1656-1662
    • Yin, S.1    Biedermannova, L.2    Dokholyan, N.V.3
  • 21
    • 70349932423 scopus 로고    scopus 로고
    • AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
    • G.M. Morris, and R. Huey A.J. Olson AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility J. Comput. Chem. 30 2009 2785 2791
    • (2009) J. Comput. Chem. , vol.30 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Olson, A.J.3
  • 25
    • 0032443390 scopus 로고    scopus 로고
    • Discrete molecular dynamics studies of the folding of a protein-like model
    • DOI 10.1016/S1359-0278(98)00072-8
    • N.V. Dokholyan, and S.V. Buldyrev E.I. Shakhnovich Discrete molecular dynamics studies of the folding of a protein-like model Fold. Des. 3 1998 577 587 (Pubitemid 29023621)
    • (1998) Folding and Design , vol.3 , Issue.6 , pp. 577-587
    • Dokholyan, N.V.1    Buldyrev, S.V.2    Stanley, H.E.3    Shakhnovich, E.I.4
  • 26
    • 46049096322 scopus 로고    scopus 로고
    • Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics
    • DOI 10.1016/j.str.2008.03.013, PII S0969212608001780
    • F. Ding, and D. Tsao N.V. Dokholyan Ab initio folding of proteins with all-atom discrete molecular dynamics Structure 16 2008 1010 1018 (Pubitemid 351899281)
    • (2008) Structure , vol.16 , Issue.7 , pp. 1010-1018
    • Ding, F.1    Tsao, D.2    Nie, H.3    Dokholyan, N.V.4
  • 27
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • P. Kollman Free energy calculations: applications to chemical and biochemical phenomena Chem. Rev. 93 1993 2395 2417
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 28
    • 0034628914 scopus 로고    scopus 로고
    • Identifying the protein folding nucleus using molecular dynamics
    • N.V. Dokholyan, and S.V. Buldyrev E.I. Shakhnovich Identifying the protein folding nucleus using molecular dynamics J. Mol. Biol. 296 2000 1183 1188
    • (2000) J. Mol. Biol. , vol.296 , pp. 1183-1188
    • Dokholyan, N.V.1    Buldyrev, S.V.2    Shakhnovich, E.I.3
  • 30
    • 77950271944 scopus 로고    scopus 로고
    • An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery
    • N. Brooijmans, and Y.W. Chang C. Humblet An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery Protein Sci. 19 2010 763 774
    • (2010) Protein Sci. , vol.19 , pp. 763-774
    • Brooijmans, N.1    Chang, Y.W.2    Humblet, C.3
  • 31
    • 45749139232 scopus 로고    scopus 로고
    • Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: Evaluation on kinase inhibitor cross docking
    • DOI 10.1021/jm800071v
    • A. May, and M. Zacharias Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking J. Med. Chem. 51 2008 3499 3506 (Pubitemid 351875006)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.12 , pp. 3499-3506
    • May, A.1    Zacharias, M.2
  • 32
    • 33646757492 scopus 로고    scopus 로고
    • On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites
    • DOI 10.1002/prot.20897
    • M. Nayal, and B. Honig On the nature of cavities on protein surfaces: application to the identification of drug-binding sites Proteins 63 2006 892 906 (Pubitemid 43765141)
    • (2006) Proteins: Structure, Function and Genetics , vol.63 , Issue.4 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 33
    • 33847770470 scopus 로고    scopus 로고
    • Multiscale modeling of nucleosome dynamics
    • DOI 10.1529/biophysj.106.094805
    • S. Sharma, F. Ding, and N.V. Dokholyan Multiscale modeling of nucleosome dynamics Biophys. J. 92 2007 1457 1470 (Pubitemid 46393459)
    • (2007) Biophysical Journal , vol.92 , Issue.5 , pp. 1457-1470
    • Sharma, S.1    Ding, F.2    Dokholyan, N.V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.