메뉴 건너뛰기




Volumn 9, Issue 10, 2014, Pages 1121-1131

The cloud and other new computational methods to improve molecular modelling

Author keywords

Cloud computing; Docking; Graphics processing units; Grid computing; Molecular dynamics; Molecular modelling; Multi core architectures; Virtual screening

Indexed keywords

ALGORITHM; CLOUD COMPUTING; COMPUTER; COMPUTER GRAPHICS; GRAPHICS PROCESSING UNIT; GRID COMPUTING; MOLECULAR DYNAMICS; MOLECULAR MODEL; REVIEW; TECHNOLOGY; THEORETICAL MODEL; BIOLOGY; DRUG DEVELOPMENT; PROCEDURES;

EID: 84907428470     PISSN: 17460441     EISSN: 1746045X     Source Type: Journal    
DOI: 10.1517/17460441.2014.941800     Document Type: Review
Times cited : (16)

References (108)
  • 1
    • 77949405791 scopus 로고    scopus 로고
    • Successful applications of computer aided drug discovery: Moving drugs from concept to the clinic
    • Talele TT, Khedkar SA, Rigby AC. Successful applications of computer aided drug discovery: moving drugs from concept to the clinic. Curr Top Med Chem 2010;10:127-41
    • (2010) Curr Top Med Chem , vol.10 , pp. 127-141
    • Talele, T.T.1    Khedkar, S.A.2    Rigby, A.C.3
  • 2
    • 10044240760 scopus 로고    scopus 로고
    • Retrieval of crystallographically-derived molecular geometry information
    • Bruno IJ, Cole JC, Kessler M, et al. Retrieval of crystallographically-derived molecular geometry information. J Chem Inf Comput Sci 2004;44:2133-44
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 2133-2144
    • Bruno, I.J.1    Cole, J.C.2    Kessler, M.3
  • 3
    • 0000793139 scopus 로고
    • Cramming more components onto integrated circuits
    • Moore G. Cramming more components onto integrated circuits. Electronics 1965;38:114-17
    • (1965) Electronics , vol.38 , pp. 114-117
    • Moore, G.1
  • 4
    • 68249091607 scopus 로고    scopus 로고
    • The impact of hardware improvement for molecular modeling in a grid environment
    • Li D, Sun M, Li M, et al. The impact of hardware improvement for molecular modeling in a grid environment. Expert Opin Drug Discov 2009;4:873-7
    • (2009) Expert Opin Drug Discov , vol.4 , pp. 873-877
    • Li, D.1    Sun, M.2    Li, M.3
  • 5
    • 45949096377 scopus 로고    scopus 로고
    • Grid computing in large pharmaceutical molecular modeling
    • Claus BL, Johnson SR. Grid computing in large pharmaceutical molecular modeling. Drug Discov Today 2008;13:578-83
    • (2008) Drug Discov Today , vol.13 , pp. 578-583
    • Claus, B.L.1    Johnson, S.R.2
  • 6
    • 77950792011 scopus 로고    scopus 로고
    • In silico drug discovery approaches on grid computing infrastructures
    • Wolf A, Shahid M, Kasam V, et al. In silico drug discovery approaches on grid computing infrastructures. Curr Clin Pharmacol 2010;5:37-46
    • (2010) Curr Clin Pharmacol , vol.5 , pp. 37-46
    • Wolf, A.1    Shahid, M.2    Kasam, V.3
  • 7
    • 38949123200 scopus 로고    scopus 로고
    • Grid-enabled virtual screening against malaria
    • Jacq N, Salzemann J, Jacq F, et al. Grid-enabled virtual screening against malaria. J Grid Comput 2008;6:29-43
    • (2008) J Grid Comput , vol.6 , pp. 29-43
    • Jacq, N.1    Salzemann, J.2    Jacq, F.3
  • 8
    • 67749097923 scopus 로고    scopus 로고
    • Design and discovery of plasmepsin II inhibitors using an automated workflow on large-scale grids
    • Degliesposti G, Kasam V, Da Costa A, et al. Design and discovery of plasmepsin II inhibitors using an automated workflow on large-scale grids. ChemMedChem 2009;4:1164-73
    • (2009) ChemMedChem , vol.4 , pp. 1164-1173
    • Degliesposti, G.1    Kasam, V.2    Da Costa, A.3
  • 9
    • 60349105674 scopus 로고    scopus 로고
    • Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening
    • Rastelli G, Degliesposti G, Del Rio A, et al. Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening. Chem Biol Drug Des 2009;73:283-6
    • (2009) Chem Biol Drug des , vol.73 , pp. 283-286
    • Rastelli, G.1    Degliesposti, G.2    Del Rio, A.3
  • 10
    • 67649191688 scopus 로고    scopus 로고
    • WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures
    • Kasam V, Salzemann J, Botha M, et al. WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures. Malar J 2009;8:88
    • (2009) Malar J , vol.8 , pp. 88
    • Kasam, V.1    Salzemann, J.2    Botha, M.3
  • 11
    • 78049348189 scopus 로고    scopus 로고
    • GVSS: A high throughput drug discovery service of avian flu and dengue fever for EGEE and EUAsiaGrid
    • Chen H-Y, Hsiung M, Lee H-C, et al. GVSS: a high throughput drug discovery service of avian flu and dengue fever for EGEE and EUAsiaGrid. J Grid Comput 2010;8:529-41
    • (2010) J Grid Comput , vol.8 , pp. 529-541
    • Chen, H.-Y.1    Hsiung, M.2    Lee, H.-C.3
  • 12
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-62
    • (1998) J Comput Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3
  • 13
    • 44449150640 scopus 로고    scopus 로고
    • Hydra: A self regenerating high performance computing grid for drug discovery
    • Bullard D, Gobbi A, Lardy MA, et al. Hydra: a self regenerating high performance computing grid for drug discovery. J Chem Inf Model 2008;48:811-16
    • (2008) J Chem Inf Model , vol.48 , pp. 811-816
    • Bullard, D.1    Gobbi, A.2    Lardy, M.A.3
  • 14
    • 39149117986 scopus 로고    scopus 로고
    • GridMol: A grid application for molecular modeling and visualization
    • Sun Y, Shen B, Lu Z, et al. GridMol: a grid application for molecular modeling and visualization. J Comput Aided Mol Des 2008;22:119-29
    • (2008) J Comput Aided Mol des , vol.22 , pp. 119-129
    • Sun, Y.1    Shen, B.2    Lu, Z.3
  • 15
    • 79953212870 scopus 로고    scopus 로고
    • Using a private desktop grid system for accelerating drug discovery
    • Kovács J, Kacsuk P, Lomaka A. Using a private desktop grid system for accelerating drug discovery. Future Gener Comput Syst 2011;27:657-66
    • (2011) Future Gener Comput Syst , vol.27 , pp. 657-666
    • Kovács, J.1    Kacsuk, P.2    Lomaka, A.3
  • 19
    • 84880182727 scopus 로고    scopus 로고
    • The emerging role of cloud computing in molecular modelling
    • Ebejer J-P, Fulle S, Morris GM, et al. The emerging role of cloud computing in molecular modelling. J Mol Graph Model 2013;44:177-87
    • (2013) J Mol Graph Model , vol.44 , pp. 177-187
    • Ebejer, J.-P.1    Fulle, S.2    Morris, G.M.3
  • 20
    • 84884883499 scopus 로고    scopus 로고
    • Cloud infrastructures for in silico drug discovery: Economic and practical aspects
    • D'Agostino D, Clematis A, Quarati A, et al. Cloud infrastructures for in silico drug discovery: economic and practical aspects. BioMed Res Int 2013;2013:1-19
    • (2013) BioMed Res Int , vol.2013 , pp. 1-19
    • D'agostino, D.1    Clematis, A.2    Quarati, A.3
  • 23
    • 84858330364 scopus 로고    scopus 로고
    • Cloud BioLinux: Pre-configured and on-demand bioinformatics computing for the genomics community
    • Krampis K, Booth T, Chapman B, et al. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics 2012;13:42
    • (2012) BMC Bioinformatics , vol.13 , pp. 42
    • Krampis, K.1    Booth, T.2    Chapman, B.3
  • 24
    • 84881507563 scopus 로고    scopus 로고
    • Cloud prediction of protein structure and function with predictprotein for Debian
    • Kajan L, Yachdav G, Vicedo E, et al. Cloud prediction of protein structure and function with predictprotein for Debian. BioMed Res Int 2013;2013:1-6
    • (2013) BioMed Res Int , vol.2013 , pp. 1-6
    • Kajan, L.1    Yachdav, G.2    Vicedo, E.3
  • 25
    • 84870057823 scopus 로고    scopus 로고
    • Bioinformatics clouds for big data manipulation
    • Dai L, Gao X, Guo Y, et al. Bioinformatics clouds for big data manipulation. Biol Direct 2012;7:43
    • (2012) Biol Direct , vol.7 , pp. 43
    • Dai, L.1    Gao, X.2    Guo, Y.3
  • 26
    • 84862192766 scopus 로고    scopus 로고
    • ChEMBL: A large-scale bioactivity database for drug discovery
    • Gaulton A, Bellis LJ, Bento AP, et al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 2012;40:D1100-7
    • (2012) Nucleic Acids Res , vol.40 , pp. D1100-D1107
    • Gaulton, A.1    Bellis, L.J.2    Bento, A.P.3
  • 27
    • 84907432633 scopus 로고    scopus 로고
    • [Last accessed 4 April 2014]
    • ChemSpider. Available from: http:// www.chemspider.com/ [Last accessed 4 April 2014]
  • 28
    • 84879602378 scopus 로고    scopus 로고
    • [Last accessed 4 April 2014]
    • Pistoia Alliance. Available from: http:// www.pistoiaalliance.org/ [Last accessed 4 April 2014]
    • Pistoia Alliance.
  • 29
    • 84868138829 scopus 로고    scopus 로고
    • Open PHACTS: Semantic interoperability for drug discovery
    • Williams AJ, Harland L, Groth P, et al. Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today 2012;17:1188-98
    • (2012) Drug Discov Today , vol.17 , pp. 1188-1198
    • Williams, A.J.1    Harland, L.2    Groth, P.3
  • 30
    • 84907432632 scopus 로고    scopus 로고
    • [Last accessed 4 April 2014]
    • OpenTox. Available from: http://www. opentox.org/ [Last accessed 4 April 2014]
  • 32
    • 84890917722 scopus 로고    scopus 로고
    • Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
    • Kohlhoff KJ, Shukla D, Lawrenz M, et al. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nat Chem 2014;6:15-21
    • (2014) Nat Chem , vol.6 , pp. 15-21
    • Kohlhoff, K.J.1    Shukla, D.2    Lawrenz, M.3
  • 33
    • 84902540331 scopus 로고    scopus 로고
    • Large-scale virtual screening experiments on Windows Azure-based cloud resources
    • Kiss T, Borsody P, Terstyanszky G, et al. Large-scale virtual screening experiments on Windows Azure-based cloud resources. Concurr Comput Pract Exp 2013;26(10):1760-70
    • (2013) Concurr Comput Pract Exp , vol.26 , Issue.10 , pp. 1760-1770
    • Kiss, T.1    Borsody, P.2    Terstyanszky, G.3
  • 34
    • 84877277360 scopus 로고    scopus 로고
    • WFReDoW: A cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model
    • De Paris R, Frantz FA, de Souza ON, et al. wFReDoW: a cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model. BioMed Res Int 2013;2013:1-12
    • (2013) BioMed Res Int , vol.2013 , pp. 1-12
    • De Paris, R.1    Frantz, F.A.2    De Souza, O.N.3
  • 35
    • 70349932423 scopus 로고    scopus 로고
    • AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
    • Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 2009;30:2785-91
    • (2009) J Comput Chem , vol.30 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Lindstrom, W.3
  • 36
    • 84907439173 scopus 로고    scopus 로고
    • [Last accessed 6 April 2014]
    • ApacheTM Hadoop-. Available from: http://hadoop.apache.org/[Last accessed 6 April 2014]
    • ApacheTM Hadoop
  • 37
    • 84894273072 scopus 로고    scopus 로고
    • High-throughput virtual molecular docking with AutoDockCloud
    • Ellingson SR, Baudry J. High-throughput virtual molecular docking with AutoDockCloud. Concurr Comput Pract Exp 2014;26:907-16
    • (2014) Concurr Comput Pract Exp , vol.26 , pp. 907-916
    • Ellingson, S.R.1    Baudry, J.2
  • 38
    • 84870818941 scopus 로고    scopus 로고
    • A Hadoop-based massive molecular data storage solution for virtual screening
    • 2012 Seventh
    • Zhang Y, Zhang R, Chen Q, et al. A Hadoop-based massive molecular data storage solution for virtual screening. In ChinaGrid Annual Conference (ChinaGrid), 2012 Seventh; 2012. p. 142-7
    • (2012) ChinaGrid Annual Conference (ChinaGrid) , pp. 142-147
    • Zhang, Y.1    Zhang, R.2    Chen, Q.3
  • 39
    • 80051545693 scopus 로고    scopus 로고
    • IScreen: World's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan
    • Tsai T-Y, Chang K-W, Chen CY. iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan. J Comput Aided Mol Des 2011;25:525-31
    • (2011) J Comput Aided Mol des , vol.25 , pp. 525-531
    • Tsai, T.-Y.1    Chang, K.-W.2    Chen, C.Y.3
  • 40
    • 84883564023 scopus 로고    scopus 로고
    • CovalentDock cloud: A web server for automated covalent docking
    • Ouyang X, Zhou S, Ge Z, et al. CovalentDock cloud: a web server for automated covalent docking. Nucleic Acids Res 2013;41:W329-32
    • (2013) Nucleic Acids Res , vol.41 , pp. W329-W332
    • Ouyang, X.1    Zhou, S.2    Ge, Z.3
  • 41
    • 77952317213 scopus 로고    scopus 로고
    • Supporting molecular modeling workflows within a grid services cloud
    • Taniar D, Gervasi O, Murgante B, Pardede E, Apduhan BO, editors. Springer, Berlin Heidelberg
    • Koehler M, Ruckenbauer M, Janciak I, et al. Supporting molecular modeling workflows within a grid services cloud. In: Taniar D, Gervasi O, Murgante B, Pardede E, Apduhan BO, editors, Computational science and its applications-ICCSA 2010. Lecture Notes in Computer Science. Springer, Berlin Heidelberg; 2010. p. 13-28
    • (2010) Computational Science and Its Applications-ICCSA 2010. Lecture Notes in Computer Science , pp. 13-28
    • Koehler, M.1    Ruckenbauer, M.2    Janciak, I.3
  • 42
    • 84896906300 scopus 로고    scopus 로고
    • A VMD plugin for NAMD simulations on Amazon EC2
    • Wong AK, Goscinski AM. A VMD plugin for NAMD simulations on Amazon EC2. Procedia Comput Sci 2012;9:136-45
    • (2012) Procedia Comput Sci , vol.9 , pp. 136-145
    • Wong, A.K.1    Goscinski, A.M.2
  • 44
    • 27344436659 scopus 로고    scopus 로고
    • Scalable molecular dynamics with NAMD
    • Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781-802
    • (2005) J Comput Chem , vol.26 , pp. 1781-1802
    • Phillips, J.C.1    Braun, R.2    Wang, W.3
  • 45
    • 84861866880 scopus 로고    scopus 로고
    • A high performance scientific cloud computing environment for materials simulations
    • Jorissen K, Vila FD, Rehr JJ. A high performance scientific cloud computing environment for materials simulations. Comput Phys Commun 2012;183:1911-19
    • (2012) Comput Phys Commun , vol.183 , pp. 1911-1919
    • Jorissen, K.1    Vila, F.D.2    Rehr, J.J.3
  • 46
    • 84876535610 scopus 로고    scopus 로고
    • Translational biomedical informatics in the cloud: Present and future
    • Chen J, Qian F, Yan W, et al. Translational biomedical informatics in the cloud: present and future. BioMed Res Int 2013;2013:1-8
    • (2013) BioMed Res Int , vol.2013 , pp. 1-8
    • Chen, J.1    Qian, F.2    Yan, W.3
  • 47
    • 78649574884 scopus 로고    scopus 로고
    • Cloud computing and validation of expandable in silico livers
    • Ropella GE, Hunt CA. Cloud computing and validation of expandable in silico livers. BMC Syst Biol 2010;4:168
    • (2010) BMC Syst Biol , vol.4 , pp. 168
    • Ropella, G.E.1    Hunt, C.A.2
  • 51
    • 77956286977 scopus 로고    scopus 로고
    • GPU-Accelerated molecular modeling coming of age
    • Stone JE, Hardy DJ, Ufimtsev IS, et al. GPU-Accelerated molecular modeling coming of age. J Mol Graph Model 2010;29:116-25
    • (2010) J Mol Graph Model , vol.29 , pp. 116-125
    • Stone, J.E.1    Hardy, D.J.2    Ufimtsev, I.S.3
  • 52
    • 77950551363 scopus 로고    scopus 로고
    • Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
    • Eastman P, Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J Comput Chem 2010;31:1268-72
    • (2010) J Comput Chem , vol.31 , pp. 1268-1272
    • Eastman, P.1    Pande, V.S.2
  • 53
    • 79960595060 scopus 로고    scopus 로고
    • Molecular dynamics simulations using graphics processing units
    • Baker JA, Hirst JD. Molecular dynamics simulations using graphics processing units. Mol Informatics 2011;30:498-504
    • (2011) Mol Informatics , vol.30 , pp. 498-504
    • Baker, J.A.1    Hirst, J.D.2
  • 54
    • 84882687075 scopus 로고    scopus 로고
    • GALAMOST: GPU-Accelerated largescale molecular simulation toolkit
    • Zhu Y-L, Liu H, Li Z-W, et al. GALAMOST: GPU-Accelerated largescale molecular simulation toolkit. J Comput Chem 2013;34:2197-211
    • (2013) J Comput Chem , vol.34 , pp. 2197-2211
    • Zhu, Y.-L.1    Liu, H.2    Li, Z.-W.3
  • 55
    • 84875546633 scopus 로고    scopus 로고
    • Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics
    • Zheng M, Li X, Guo L. Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics. J Mol Graph Model 2013;41:1-11
    • (2013) J Mol Graph Model , vol.41 , pp. 1-11
    • Zheng, M.1    Li, X.2    Guo, L.3
  • 56
    • 84892726544 scopus 로고    scopus 로고
    • Pyrolysis of Liulin coal simulated by GPU-based ReaxFF MD with cheminformatics analysis
    • Zheng M, Li X, Liu J, et al. Pyrolysis of Liulin coal simulated by GPU-based ReaxFF MD with cheminformatics analysis. Energy Fuels 2014;28:522-34
    • (2014) Energy Fuels , vol.28 , pp. 522-534
    • Zheng, M.1    Li, X.2    Liu, J.3
  • 57
    • 77749298172 scopus 로고    scopus 로고
    • Current status of the AMOEBA polarizable force field
    • Ponder JW, Wu C, Ren P, et al. Current status of the AMOEBA polarizable force field. J Phys Chem B 2010;114:2549-64
    • (2010) J Phys Chem B , vol.114 , pp. 2549-2564
    • Ponder, J.W.1    Wu, C.2    Ren, P.3
  • 58
    • 85008042563 scopus 로고    scopus 로고
    • OpenMM: A hardware-independent framework for molecular simulations
    • Eastman P, Pande V. OpenMM: a hardware-independent framework for molecular simulations. Comput Sci Eng 2010;12:34-9
    • (2010) Comput Sci Eng , vol.12 , pp. 34-39
    • Eastman, P.1    Pande, V.2
  • 59
    • 84872152631 scopus 로고    scopus 로고
    • OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation
    • Eastman P, Friedrichs MS, Chodera JD, et al. OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation. J Chem Theory Comput 2013;9:461-9
    • (2013) J Chem Theory Comput , vol.9 , pp. 461-469
    • Eastman, P.1    Friedrichs, M.S.2    Chodera, J.D.3
  • 60
    • 84887852425 scopus 로고    scopus 로고
    • Accelerated molecular dynamics simulations with the AMOEBA polarizable force field on graphics processing units
    • Lindert S, Bucher D, Eastman P, et al. Accelerated molecular dynamics simulations with the AMOEBA polarizable force field on graphics processing units. J Chem Theory Comput 2013;9:4684-91
    • (2013) J Chem Theory Comput , vol.9 , pp. 4684-4691
    • Lindert, S.1    Bucher, D.2    Eastman, P.3
  • 61
    • 41249087856 scopus 로고    scopus 로고
    • General purpose molecular dynamics simulations fully implemented on graphics processing units
    • Anderson JA, Lorenz CD, Travesset A. General purpose molecular dynamics simulations fully implemented on graphics processing units. J Comput Phys 2008;227:5342-59
    • (2008) J Comput Phys , vol.227 , pp. 5342-5359
    • Anderson, J.A.1    Lorenz, C.D.2    Travesset, A.3
  • 62
    • 83455244929 scopus 로고    scopus 로고
    • Micellization studied by GPUaccelerated coarse-grained molecular dynamics
    • Levine BG, LeBard DN, DeVane R, et al. Micellization studied by GPUaccelerated coarse-grained molecular dynamics. J Chem Theory Comput 2011;7:4135-45
    • (2011) J Chem Theory Comput , vol.7 , pp. 4135-4145
    • Levine, B.G.1    Lebard, D.N.2    Devane, R.3
  • 63
    • 84875451264 scopus 로고    scopus 로고
    • Fragment-based drug discovery using a multidomain, parallel MD-MM/ PBSA screening protocol
    • Zhu T, Lee H, Lei H, et al. Fragment-based drug discovery using a multidomain, parallel MD-MM/ PBSA screening protocol. J Chem Inf Model 2013;53:560-72
    • (2013) J Chem Inf Model , vol.53 , pp. 560-572
    • Zhu, T.1    Lee, H.2    Lei, H.3
  • 64
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones G, Willett P, Glen RC. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 1995;245:43-53
    • (1995) J Mol Biol , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 65
    • 23444454552 scopus 로고    scopus 로고
    • The Amber biomolecular simulation programs
    • Case DA, Cheatham TE, Darden T, et al. The Amber biomolecular simulation programs. J Comput Chem 2005;26:1668-88
    • (2005) J Comput Chem , vol.26 , pp. 1668-1688
    • Case, D.A.1    Cheatham, T.E.2    Darden, T.3
  • 66
    • 84884192184 scopus 로고    scopus 로고
    • Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald
    • Salomon-Ferrer R, Gotz AW, Poole D, et al. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. explicit solvent particle mesh Ewald. J Chem Theory Comput 2013;9:3878-88
    • (2013) J Chem Theory Comput , vol.9 , pp. 3878-3888
    • Salomon-Ferrer, R.1    Gotz, A.W.2    Poole, D.3
  • 67
    • 84860767348 scopus 로고    scopus 로고
    • Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born
    • Gotz AW, Williamson MJ, Xu D, et al. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput 2012;8:1542-55
    • (2012) J Chem Theory Comput , vol.8 , pp. 1542-1555
    • Gotz, A.W.1    Williamson, M.J.2    Xu, D.3
  • 68
    • 84887043744 scopus 로고    scopus 로고
    • Molecular dynamics-based virtual screening: Accelerating the drug discovery process by high-performance computing
    • Ge H, Wang Y, Li C, et al. Molecular dynamics-based virtual screening: accelerating the drug discovery process by high-performance computing. J Chem Inf Model 2013;53:2757-64
    • (2013) J Chem Inf Model , vol.53 , pp. 2757-2764
    • Ge, H.1    Wang, Y.2    Li, C.3
  • 69
    • 79959211957 scopus 로고    scopus 로고
    • Accelerating all-Atom normal mode analysis with graphics processing unit
    • Liu L, Liu X, Gong J, et al. Accelerating all-Atom normal mode analysis with graphics processing unit. J Chem Theory Comput 2011;7:1595-603
    • (2011) J Chem Theory Comput , vol.7 , pp. 1595-1603
    • Liu, L.1    Liu, X.2    Gong, J.3
  • 70
    • 84870584806 scopus 로고    scopus 로고
    • A fast parallel clustering algorithm for molecular simulation trajectories
    • Zhao Y, Sheong FK, Sun J, et al. A fast parallel clustering algorithm for molecular simulation trajectories. J Comput Chem 2013;34:95-104
    • (2013) J Comput Chem , vol.34 , pp. 95-104
    • Zhao, Y.1    Sheong, F.K.2    Sun, J.3
  • 71
    • 84883256092 scopus 로고    scopus 로고
    • Accelerated conformational entropy calculations using graphic processing units
    • Zhang Q, Wang J, Guerrero GD, et al. Accelerated conformational entropy calculations using graphic processing units. J Chem Inf Model 2013;53:2057-64
    • (2013) J Chem Inf Model , vol.53 , pp. 2057-2064
    • Zhang, Q.1    Wang, J.2    Guerrero, G.D.3
  • 72
    • 79955407842 scopus 로고    scopus 로고
    • Accelerating molecular docking calculations using graphics processing units
    • Korb O, Stützle T, Exner TE. Accelerating molecular docking calculations using graphics processing units. J Chem Inf Model 2011;51:865-76
    • (2011) J Chem Inf Model , vol.51 , pp. 865-876
    • Korb, O.1    Stützle, T.2    Exner, T.E.3
  • 75
    • 84860492894 scopus 로고    scopus 로고
    • A GPU-based approach to accelerate computational protein-DNA docking
    • Wu J, Chen C, Hong B. A GPU-based approach to accelerate computational protein-DNA docking. Comput Sci Eng 2012;14:20-9
    • (2012) Comput Sci Eng , vol.14 , pp. 20-29
    • Wu, J.1    Chen, C.2    Hong, B.3
  • 79
    • 84864199587 scopus 로고    scopus 로고
    • ZINC: A free tool to discover chemistry for biology
    • Irwin JJ, Sterling T, Mysinger MM, et al. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 2012;52:1757-68
    • (2012) J Chem Inf Model , vol.52 , pp. 1757-1768
    • Irwin, J.J.1    Sterling, T.2    Mysinger, M.M.3
  • 81
    • 84891852541 scopus 로고    scopus 로고
    • Identifying ligand binding sites and poses using GPU-Accelerated Hamiltonian replica exchange molecular dynamics
    • Wang K, Chodera JD, Yang Y, et al. Identifying ligand binding sites and poses using GPU-Accelerated Hamiltonian replica exchange molecular dynamics. J Comput Aided Mol Des 2013;27:989-1007
    • (2013) J Comput Aided Mol des , vol.27 , pp. 989-1007
    • Wang, K.1    Chodera, J.D.2    Yang, Y.3
  • 82
    • 84864945671 scopus 로고    scopus 로고
    • LNA: Fast protein structural comparison using a Laplacian characterization of tertiary structure
    • Bonnel N, Marteau PF. LNA: Fast protein structural comparison using a Laplacian characterization of tertiary structure. IEEE/ACM Trans Comput Biol Bioinform 2012;9:1451-8
    • (2012) IEEE/ACM Trans Comput Biol Bioinform , vol.9 , pp. 1451-1458
    • Bonnel, N.1    Marteau, P.F.2
  • 83
    • 80051992077 scopus 로고    scopus 로고
    • Accelerating chemical database searching using graphics processing units
    • Liu P, Agrafiotis DK, Rassokhin DN, et al. Accelerating chemical database searching using graphics processing units. J Chem Inf Model 2011;51:1807-16
    • (2011) J Chem Inf Model , vol.51 , pp. 1807-1816
    • Liu, P.1    Agrafiotis, D.K.2    Rassokhin, D.N.3
  • 84
    • 54949108677 scopus 로고    scopus 로고
    • PubChem: Integrated platform of small molecules and biological activities
    • Wheeler RA, Spellmeyer DC, editors. Elsevier, Amsterdam, Netherlands
    • Bolton EE, Wang Y, Thiessen PA, et al. PubChem: integrated platform of small molecules and biological activities. In: Wheeler RA, Spellmeyer DC, editors, Annual reports in computational chemistry. Volume 4. Elsevier, Amsterdam, Netherlands; 2008. p. 217-41
    • (2008) Annual Reports in Computational Chemistry , vol.4 , pp. 217-241
    • Bolton, E.E.1    Wang, Y.2    Thiessen, P.A.3
  • 85
    • 73349088447 scopus 로고    scopus 로고
    • GPU accelerated support vector machines for mining high-throughput screening data
    • Liao Q, Wang J, Webster Y, et al. GPU accelerated support vector machines for mining high-throughput screening data. J Chem Inf Model 2009;49:2718-25
    • (2009) J Chem Inf Model , vol.49 , pp. 2718-2725
    • Liao, Q.1    Wang, J.2    Webster, Y.3
  • 86
    • 79960275000 scopus 로고    scopus 로고
    • Accelerating two algorithms for largescale compound selection on GPUs
    • Liao Q, Wang J, Watson IA. Accelerating two algorithms for largescale compound selection on GPUs. J Chem Inf Model 2011;51:1017-24
    • (2011) J Chem Inf Model , vol.51 , pp. 1017-1024
    • Liao, Q.1    Wang, J.2    Watson, I.A.3
  • 87
    • 79960741112 scopus 로고    scopus 로고
    • GPU accelerated chemical similarity calculation for compound library comparison
    • Ma C, Wang L, Xie X-Q. GPU accelerated chemical similarity calculation for compound library comparison. J Chem Inf Model 2011;51:1521-7
    • (2011) J Chem Inf Model , vol.51 , pp. 1521-1527
    • Ma, C.1    Wang, L.2    Xie, X.-Q.3
  • 88
    • 84867637262 scopus 로고    scopus 로고
    • Ab initio quantum chemistry for protein structures
    • Kulik HJ, Luehr N, Ufimtsev IS, et al. Ab initio quantum chemistry for protein structures. J Phys Chem B 2012;116:12501-9
    • (2012) J Phys Chem B , vol.116 , pp. 12501-12509
    • Kulik, H.J.1    Luehr, N.2    Ufimtsev, I.S.3
  • 89
    • 84870939227 scopus 로고    scopus 로고
    • Electronic absorption spectra from MM and Ab initio QM/MM molecular dynamics: Environmental effects on the absorption spectrum of photoactive yellow protein
    • Isborn CM, Gotz AW, Clark MA, et al. Electronic absorption spectra from MM and Ab initio QM/MM molecular dynamics: environmental effects on the absorption spectrum of photoactive yellow protein. J Chem Theory Comput 2012;8:5092-106
    • (2012) J Chem Theory Comput , vol.8 , pp. 5092-5106
    • Isborn, C.M.1    Gotz, A.W.2    Clark, M.A.3
  • 90
    • 79959271947 scopus 로고    scopus 로고
    • Excited-state electronic structure with configuration interaction singles and Tamm-Dancoff time-dependent density functional theory on graphical processing units
    • Isborn CM, Luehr N, Ufimtsev IS, et al. Excited-state electronic structure with configuration interaction singles and Tamm-Dancoff time-dependent density functional theory on graphical processing units. J Chem Theory Comput 2011;7:1814-23
    • (2011) J Chem Theory Comput , vol.7 , pp. 1814-1823
    • Isborn, C.M.1    Luehr, N.2    Ufimtsev, I.S.3
  • 91
    • 84872161831 scopus 로고    scopus 로고
    • Generating efficient quantum chemistry codes for novel architectures
    • Titov AV, Ufimtsev IS, Luehr N, et al. Generating efficient quantum chemistry codes for novel architectures. J Chem Theory Comput 2013;9:213-21
    • (2013) J Chem Theory Comput , vol.9 , pp. 213-221
    • Titov, A.V.1    Ufimtsev, I.S.2    Luehr, N.3
  • 92
    • 84869206889 scopus 로고    scopus 로고
    • Accelerating VASP electronic structure calculations using graphic processing units
    • Hacene M, Anciaux-Sedrakian A, Rozanska X, et al. Accelerating VASP electronic structure calculations using graphic processing units. J Comput Chem 2012;33:2581-9
    • (2012) J Comput Chem , vol.33 , pp. 2581-2589
    • Hacene, M.1    Anciaux-Sedrakian, A.2    Rozanska, X.3
  • 93
    • 84858159097 scopus 로고    scopus 로고
    • VASP on a GPU: Application to exact-exchange calculations of the stability of elemental boron
    • Hutchinson M, Widom M. VASP on a GPU: application to exact-exchange calculations of the stability of elemental boron. Comput Phys Commun 2012;183:1422-6
    • (2012) Comput Phys Commun , vol.183 , pp. 1422-1426
    • Hutchinson, M.1    Widom, M.2
  • 94
    • 79958242136 scopus 로고    scopus 로고
    • Acceleration of the GAMESS-UK electronic structure package on graphical processing units
    • Wilkinson KA, Sherwood P, Guest MF, et al. Acceleration of the GAMESS-UK electronic structure package on graphical processing units. J Comput Chem 2011;32:2313-18
    • (2011) J Comput Chem , vol.32 , pp. 2313-2318
    • Wilkinson, K.A.1    Sherwood, P.2    Guest, M.F.3
  • 95
    • 84882293282 scopus 로고    scopus 로고
    • Fast and flexible coupled cluster implementation
    • Asadchev A, Gordon MS. Fast and flexible coupled cluster implementation. J Chem Theory Comput 2013;9:3385-92
    • (2013) J Chem Theory Comput , vol.9 , pp. 3385-3392
    • Asadchev, A.1    Gordon, M.S.2
  • 96
    • 79955926729 scopus 로고    scopus 로고
    • GPU-based implementations of the noniterative regularized-CCSD(T) corrections: Applications to strongly correlated systems
    • Ma W, Krishnamoorthy S, Villa O, et al. GPU-based implementations of the noniterative regularized-CCSD(T) corrections: applications to strongly correlated systems. J Chem Theory Comput 2011;7:1316-27
    • (2011) J Chem Theory Comput , vol.7 , pp. 1316-1327
    • Ma, W.1    Krishnamoorthy, S.2    Villa, O.3
  • 97
    • 84866184290 scopus 로고    scopus 로고
    • GPU linear algebra libraries and GPGPU programming for accelerating MOPAC semiempirical quantum chemistry calculations
    • Maia JD, Urquiza Carvalho GA, Mangueira CP, et al. GPU linear algebra libraries and GPGPU programming for accelerating MOPAC semiempirical quantum chemistry calculations. J Chem Theory Comput 2012;8:3072-81
    • (2012) J Chem Theory Comput , vol.8 , pp. 3072-3081
    • Maia, J.D.1    Urquiza Carvalho, G.A.2    Mangueira, C.P.3
  • 98
    • 79952464773 scopus 로고    scopus 로고
    • GPU-powered tools boost molecular visualization
    • Chavent M, Levy B, Krone M, et al. GPU-powered tools boost molecular visualization. Brief Bioinform 2011;12:689-701
    • (2011) Brief Bioinform , vol.12 , pp. 689-701
    • Chavent, M.1    Levy, B.2    Krone, M.3
  • 100
    • 63049121693 scopus 로고    scopus 로고
    • Fast GPUbased adaptive tessellation with CUDA
    • Schwarz M, Stamminger M. Fast GPUbased adaptive tessellation with CUDA. Comput Graph Forum 2009;28:365-74
    • (2009) Comput Graph Forum , vol.28 , pp. 365-374
    • Schwarz, M.1    Stamminger, M.2
  • 101
    • 84907428452 scopus 로고    scopus 로고
    • [Last accessed 8 April 2014]
    • CUDA GPUs j NVIDIA developer zone. Available from: https://developer.nvidia. com/cuda-gpus [Last accessed 8 April 2014]
    • CUDA GPUs J NVIDIA Developer Zone
  • 105
    • 84887422413 scopus 로고    scopus 로고
    • [Last accessed 6 April 2014]
    • Intel- Xeon PhiTM product family. Available from: http://www.intel.com/ content/www/us/en/processors/xeon/xeonphi-detail.html [Last accessed 6 April 2014]
    • Intel- Xeon PhiTM Product Family
  • 106
    • 84907426363 scopus 로고    scopus 로고
    • [Last accessed 6 April 2014]
    • Nimbix accelerated compute cloud. Available from: http://www.nimbix.net [Last accessed 6 April 2014]
    • Nimbix Accelerated Compute Cloud


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.