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Volumn 53, Issue 10, 2013, Pages 2757-2764

Molecular dynamics-based virtual screening: Accelerating the drug discovery process by high-performance computing

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

EID: 84887043744     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400391s     Document Type: Article
Times cited : (59)

References (31)
  • 1
    • 84861517739 scopus 로고    scopus 로고
    • On the value of homology models for virtual screening: Discovering hCXCR3 antagonists by pharmacophore-based and structure-based approaches
    • Huang, D. N.; Gu, Q.; Hu, G.; Ye, J. M.; Salam, N. K.; Hagler, A.; Chen, H. Z.; Xu, J. On the value of homology models for virtual screening: discovering hCXCR3 antagonists by pharmacophore-based and structure-based approaches J. Chem. Inf. Model. 2012, 52, 1356-1366
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 1356-1366
    • Huang, D.N.1    Gu, Q.2    Hu, G.3    Ye, J.M.4    Salam, N.K.5    Hagler, A.6    Chen, H.Z.7    Xu, J.8
  • 2
    • 43849093505 scopus 로고    scopus 로고
    • Ten-microsecond molecular dynamics simulation of a fast-folding WW domain
    • Freddolino, P. L.; Liu, F.; Gruebele, M.; Schulten, K. Ten-microsecond molecular dynamics simulation of a fast-folding WW domain Biophys. J. 2008, 94, L75-L77
    • (2008) Biophys. J. , vol.94
    • Freddolino, P.L.1    Liu, F.2    Gruebele, M.3    Schulten, K.4
  • 3
    • 77950503976 scopus 로고    scopus 로고
    • Virtual screening: An endless staircase?
    • Schneider, G. Virtual screening: an endless staircase? Nat. Rev. Drug Discovery 2010, 9, 273-276
    • (2010) Nat. Rev. Drug Discovery , vol.9 , pp. 273-276
    • Schneider, G.1
  • 7
    • 37249079751 scopus 로고    scopus 로고
    • Line-by-line spectroscopic simulations on graphics processing units
    • Collange, S.; Daumas, M.; Defour, D. Line-by-line spectroscopic simulations on graphics processing units Comput. Phys. Commun. 2008, 178, 135-143
    • (2008) Comput. Phys. Commun. , vol.178 , pp. 135-143
    • Collange, S.1    Daumas, M.2    Defour, D.3
  • 8
    • 35148867733 scopus 로고    scopus 로고
    • High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA
    • Belleman, R. G.; Bedorf, J.; Zwart, S. F. P. High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA New Astron. 2008, 13, 103-112
    • (2008) New Astron. , vol.13 , pp. 103-112
    • Belleman, R.G.1    Bedorf, J.2    Zwart, S.F.P.3
  • 10
    • 38849131252 scopus 로고    scopus 로고
    • High-throughput sequence alignment using graphics processing units
    • Schatz, M. C.; Trapnell, C.; Delcher, A. L.; Varshney, A. High-throughput sequence alignment using graphics processing units BMC Bioinf. 2007, 8, 474
    • (2007) BMC Bioinf. , vol.8 , pp. 474
    • Schatz, M.C.1    Trapnell, C.2    Delcher, A.L.3    Varshney, A.4
  • 12
    • 84986518863 scopus 로고
    • Amber-assisted model-building with energy refinement - A general program for modeling molecules and their interactions
    • Weiner, P. K.; Kollman, P. A. Amber-assisted model-building with energy refinement-a general program for modeling molecules and their interactions J. Comput. Chem. 1981, 2, 287-303
    • (1981) J. Comput. Chem. , vol.2 , pp. 287-303
    • Weiner, P.K.1    Kollman, P.A.2
  • 13
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 18
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 19
    • 0000473453 scopus 로고    scopus 로고
    • A smooth-particle mesh Ewald method for DL-POLY molecular dynamics simulation package on the Fujitsu VPP700
    • Kholmurodov, K.; Smith, W.; Yasuoka, K.; Darden, T.; Ebisuzaki, T. A smooth-particle mesh Ewald method for DL-POLY molecular dynamics simulation package on the Fujitsu VPP700 J. Comput. Chem. 2000, 21, 1187-1191
    • (2000) J. Comput. Chem. , vol.21 , pp. 1187-1191
    • Kholmurodov, K.1    Smith, W.2    Yasuoka, K.3    Darden, T.4    Ebisuzaki, T.5
  • 20
    • 79952588669 scopus 로고    scopus 로고
    • Assessing the performance of the MM/PBSA and MM/GBSA Methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
    • Hou, T. J.; Wang, J. M.; Li, Y. Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA Methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations J. Chem. Inf. Model. 2011, 51, 69-82
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 69-82
    • Hou, T.J.1    Wang, J.M.2    Li, Y.Y.3    Wang, W.4
  • 22
    • 0037571112 scopus 로고    scopus 로고
    • Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
    • Halgren, T. A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 J. Comput. Chem. 1996, 17, 490-519
    • (1996) J. Comput. Chem. , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 24
    • 1642310340 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    • Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J. Med. Chem. 2004, 47, 1750-1759
    • (2004) J. Med. Chem. , vol.47 , pp. 1750-1759
    • Halgren, T.A.1    Murphy, R.B.2    Friesner, R.A.3    Beard, H.S.4    Frye, L.L.5    Pollard, W.T.6    Banks, J.L.7
  • 25
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities Nucleic Acids Res. 2007, 35, D198-201
    • (2007) Nucleic Acids Res. , vol.35 , pp. 198-201
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 26
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking J. Med. Chem. 2006, 49, 6789-6801
    • (2006) J. Med. Chem. , vol.49 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 27
    • 33644912316 scopus 로고    scopus 로고
    • Measuring diagnostic and predictive accuracy in disease management: An introduction to receiver operating characteristic (ROC) analysis
    • Linden, A. Measuring diagnostic and predictive accuracy in disease management: an introduction to receiver operating characteristic (ROC) analysis J. Eval. Clin. Pract. 2006, 12, 132-139
    • (2006) J. Eval. Clin. Pract. , vol.12 , pp. 132-139
    • Linden, A.1
  • 28
    • 41349093326 scopus 로고    scopus 로고
    • What do we know and when do we know it?
    • Nicholls, A. What do we know and when do we know it? J. Comput. Aided Mol. Des. 2008, 22, 239-255
    • (2008) J. Comput. Aided Mol. Des. , vol.22 , pp. 239-255
    • Nicholls, A.1
  • 29
    • 34247272948 scopus 로고    scopus 로고
    • Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem
    • Truchon, J. F.; Bayly, C. I. Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem J. Chem. Inf. Model. 2007, 47, 488-508
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 488-508
    • Truchon, J.F.1    Bayly, C.I.2
  • 30
    • 77957820654 scopus 로고    scopus 로고
    • Virtual screening for HIV protease inhibitors: A comparison of AutoDock 4 and Vina
    • Chang, M. W.; Ayeni, C.; Breuer, S.; Torbett, B. E. Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina PLoS One 2010, 5, e11955
    • (2010) PLoS One , vol.5 , pp. 11955
    • Chang, M.W.1    Ayeni, C.2    Breuer, S.3    Torbett, B.E.4
  • 31
    • 84876516249 scopus 로고    scopus 로고
    • Identification of novel phosphodiesterase-4D inhibitors prescreened by molecular dynamics-augmented modeling and validated by bioassay
    • Li, Z.; Cai, Y. H.; Cheng, Y. K.; Lu, X.; Shao, Y. X.; Li, X.; Liu, M.; Liu, P.; Luo, H. B. Identification of novel phosphodiesterase-4D inhibitors prescreened by molecular dynamics-augmented modeling and validated by bioassay J. Chem. Inf. Model. 2013, 53, 972-981
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 972-981
    • Li, Z.1    Cai, Y.H.2    Cheng, Y.K.3    Lu, X.4    Shao, Y.X.5    Li, X.6    Liu, M.7    Liu, P.8    Luo, H.B.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.