메뉴 건너뛰기




Volumn 24, Issue 5, 2010, Pages 417-422

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

Author keywords

Autodock; Docking; PyMOL; Vina; Virtual screening

Indexed keywords

BINDING SITES;

EID: 77953325845     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9352-6     Document Type: Article
Times cited : (1619)

References (17)
  • 1
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • DOI 10.1038/nrd1549
    • D Kitchen H Decornez J Furr J Bajorath 2004 Docking and scoring in virtual screening for drug discovery: methods and applications Nat Rev Drug Discov 3 11 935 949 10.1038/nrd1549 1:CAS:528:DC%2BD2cXptFemtrg%3D (Pubitemid 39529931)
    • (2004) Nature Reviews Drug Discovery , vol.3 , Issue.11 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 5
    • 33847142225 scopus 로고    scopus 로고
    • CAVER: A new tool to explore routes from protein clefts, pockets and cavities
    • DOI 10.1186/1471-2105-7-316
    • M Petřek M Otyepka P Banáš P Košinová J Koča J Damborský 2006 CAVER: a new tool to explore routes from protein clefts, pockets and cavities BMC Bioinformatics 7 1 316 10.1186/1471-2105-7-316 (Pubitemid 46277092)
    • (2006) BMC Bioinformatics , vol.7 , pp. 316
    • Petrek, M.1    Otyepka, M.2    Banas, P.3    Kosinova, P.4    Koca, J.5    Damborsky, J.6
  • 6
    • 33847076903 scopus 로고    scopus 로고
    • Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles
    • DOI 10.1002/biot.200600208
    • J Damborsky M Petrek P Banáš M Otyepka 2007 Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles Biotechnol J 2 62 67 10.1002/biot.200600208 (Pubitemid 46744756)
    • (2007) Biotechnology Journal , vol.2 , Issue.1 , pp. 62-67
    • Damborsky, J.1    Petrek, M.2    Banas, P.3    Otyepka, M.4
  • 7
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • 10.1002/pro.5560070905 1:CAS:528:DyaK1cXmtFGjsLo%3D
    • J Liang H Edelsbrunner C Woodward 1998 Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design Protein Sci 7 1884 1897 10.1002/pro.5560070905 1:CAS:528: DyaK1cXmtFGjsLo%3D
    • (1998) Protein Sci , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 8
    • 0032189626 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
    • DOI 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H
    • J Liang H Edelsbrunner P Fu P Sudhakar S Subramaniam 1998 Analytical shape computing of macromolecules II: identification and computation of inaccessible cavities inside proteins Proteins: Struct Funct Genet 33 18 29 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H 1:CAS:528:DyaK1cXlvFCis70%3D (Pubitemid 28413010)
    • (1998) Proteins: Structure, Function and Genetics , vol.33 , Issue.1 , pp. 18-29
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 9
    • 0032190305 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
    • DOI 10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O
    • J Liang H Edelsbrunner P Fu P Sudhakar S Subramaniam 1998 Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape Proteins: Struct. Funct. Genet. 33 1 1 17 10.1002/(SICI)1097- 0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O 1:CAS:528:DyaK1cXlvFCis7w%3D (Pubitemid 28413009)
    • (1998) Proteins: Structure, Function and Genetics , vol.33 , Issue.1 , pp. 1-17
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 10
    • 34247868161 scopus 로고    scopus 로고
    • EMovie: A storyboard-based tool for making molecular movies
    • DOI 10.1016/j.tibs.2007.03.008, PII S0968000407000655
    • E Hodis G Schreiber K Rother J Sussman 2007 eMovie: a storyboard-based tool for making molecular movies Trends Biochem Sci 32 5 199 204 10.1016/j.tibs.2007.03.008 1:CAS:528:DC%2BD2sXlt1aisbo%3D (Pubitemid 46694333)
    • (2007) Trends in Biochemical Sciences , vol.32 , Issue.5 , pp. 199-204
    • Hodis, E.1    Schreiber, G.2    Rother, K.3    Sussman, J.L.4
  • 11
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a lamarckian genetic algorithm and and empirical binding free energy function
    • 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B 1:CAS:528:DyaK1cXntFemur4%3D
    • GM Morris DS Goodsell DS Halliday R Huey WE Hart R Belew AJ Olson 1998 Automated docking using a lamarckian genetic algorithm and and empirical binding free energy function J Comp Chem 19 1639 1662 10.1002/(SICI)1096-987X(19981115) 19:14<1639::AID-JCC10>3.0.CO;2-B 1:CAS:528:DyaK1cXntFemur4%3D
    • (1998) J Comp Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, D.S.3    Huey, R.4    Hart, W.E.5    Belew, R.6    Olson, A.J.7
  • 12
    • 33947716119 scopus 로고    scopus 로고
    • Software news and update a semiempirical free energy force field with charge-based desolvation
    • DOI 10.1002/jcc.20634
    • R Huey GM Morris AJ Olson DS Goodsell 2007 A semiempirical free energy force field with charge-based desolvation J Comp Chem 28 1145 1152 10.1002/jcc.20634 1:CAS:528:DC%2BD2sXjsVSms78%3D (Pubitemid 46506716)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.6 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 13
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • 1:CAS:528:DC%2BD1MXhsFGnur3O
    • O Trott A Olson 2010 AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J Comp Chem 31 455 461 1:CAS:528:DC%2BD1MXhsFGnur3O
    • (2010) J Comp Chem , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.2
  • 14
    • 0033397980 scopus 로고    scopus 로고
    • Python: A programming language for software integration and development
    • 1:CAS:528:DC%2BD3cXhtV2rsA%3D%3D
    • M Sanner 1999 Python: a programming language for software integration and development J Mol Graphics Mod 17 57 61 1:CAS:528:DC%2BD3cXhtV2rsA%3D%3D
    • (1999) J Mol Graphics Mod , vol.17 , pp. 57-61
    • Sanner, M.1
  • 15
    • 33748173818 scopus 로고    scopus 로고
    • BDT: An easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
    • DOI 10.1093/bioinformatics/btl197
    • M Vaque A Arola C Aliagas G Pujadas 2006 BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock Bioinformatics 22 14 1803 10.1093/bioinformatics/btl197 1:CAS:528:DC%2BD28Xotl2rtr0%3D (Pubitemid 44307817)
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. 1803-1804
    • Vaque, M.1    Arola, A.2    Aliagas, C.3    Pujadas, G.4
  • 16
    • 40749120187 scopus 로고    scopus 로고
    • DOVIS: An implementation for high-throughput virtual screening using AutoDock
    • DOI 10.1186/1471-2105-9-126
    • S Zhang K Kumar X Jiang A Wallqvist J Reifman 2008 DOVIS: an implementation for high-throughput virtual screening using AutoDock Bmc Bioinformatics 9 1 126 10.1186/1471-2105-9-126 (Pubitemid 351386975)
    • (2008) BMC Bioinformatics , vol.9 , pp. 126
    • Zhang, S.1    Kumar, K.2    Jiang, X.3    Wallqvist, A.4    Reifman, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.