메뉴 건너뛰기




Volumn 16, Issue 5, 2010, Pages 903-913

A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity

Author keywords

Combinatorial optimization; Docking; Hydrogen bond matching; Virtual screening

Indexed keywords

LIGAND; PROTEIN;

EID: 77953955973     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-009-0598-7     Document Type: Article
Times cited : (28)

References (32)
  • 1
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris GM et al (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662.
    • (1998) J Comput Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1
  • 4
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G et al (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748.
    • (1997) J Mol Biol , vol.267 , pp. 727-748
    • Jones, G.1
  • 6
    • 0345483185 scopus 로고    scopus 로고
    • Prodock: software package for protein modeling and docking
    • Trosset J, Scheraga H (1999) Prodock: software package for protein modeling and docking. J Comput Chem 20:412-427.
    • (1999) J Comput Chem , vol.20 , pp. 412-427
    • Trosset, J.1    Scheraga, H.2
  • 7
    • 84986522918 scopus 로고
    • ICM-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation
    • Abagyan R, Totrov M, Kuznetsov D (1994) ICM-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488-506.
    • (1994) J Comput Chem , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 8
    • 0032855301 scopus 로고    scopus 로고
    • MCDOCK: a Monte Carlo simulation approach to the molecular docking problem
    • Liu M, Wang S (1999) MCDOCK: a Monte Carlo simulation approach to the molecular docking problem. J Comput Aided Mol Des 13:435-451.
    • (1999) J Comput Aided Mol des , vol.13 , pp. 435-451
    • Liu, M.1    Wang, S.2
  • 10
    • 0031181346 scopus 로고    scopus 로고
    • QXP: powerful, rapid computer algorithms for structure-based drug design
    • McMartin C, Bohacek R (1997) QXP: powerful, rapid computer algorithms for structure-based drug design. J Comput Aided Mol Des 11:333-344.
    • (1997) J Comput Aided Mol des , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.2
  • 11
    • 0032533791 scopus 로고    scopus 로고
    • Flexible docking using Tabu search and an empirical estimate of binding affinity
    • Baxter CA et al (1998) Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins: Structure, Function, and Genetics 33:367-382.
    • (1998) Proteins: Structure, Function, and Genetics , vol.33 , pp. 367-382
    • Baxter, C.A.1
  • 12
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases
    • Ewing TJA, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15:411-428.
    • (2001) J Comput Aided Mol des , vol.15 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 13
    • 0027027467 scopus 로고
    • LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
    • Bohm H (1992) LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 6:593-606.
    • (1992) J Comput Aided Mol des , vol.6 , pp. 593-606
    • Bohm, H.1
  • 14
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489.
    • (1996) J Mol Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 15
    • 0027985242 scopus 로고
    • Rational automatic search method for stable docking models of protein and ligand
    • Mizutani M, Tomioka N, Itai A (1994) Rational automatic search method for stable docking models of protein and ligand. J Mol Biol 243:310-326.
    • (1994) J Mol Biol , vol.243 , pp. 310-326
    • Mizutani, M.1    Tomioka, N.2    Itai, A.3
  • 16
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites
    • Welch W, Ruppert J, Jain A (1996) Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 3:449-462.
    • (1996) Chem Biol , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.3
  • 17
    • 0028412035 scopus 로고
    • FLOG: a system to select 'quasi-flexible'ligands complementary to a receptor of known three-dimensional structure
    • Miller M, Kearsley S, Underwood D, Sheridan R (1994) FLOG: a system to select 'quasi-flexible'ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 8:153-174.
    • (1994) J Comput Aided Mol des , vol.8 , pp. 153-174
    • Miller, M.1    Kearsley, S.2    Underwood, D.3    Sheridan, R.4
  • 18
    • 84988103838 scopus 로고
    • Empirical energy functions for energy minimization and dynamics of nucleic acids Supported in part by a grant from the national institutes of health
    • Nilsson L, Karplus M (1986) Empirical energy functions for energy minimization and dynamics of nucleic acids Supported in part by a grant from the national institutes of health. J Comput Chem 7:591-616.
    • (1986) J Comput Chem , vol.7 , pp. 591-616
    • Nilsson, L.1    Karplus, M.2
  • 19
    • 84986518863 scopus 로고
    • AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
    • Weiner P, Kollman P (1981) AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions. J Comput Chem 2:287-303.
    • (1981) J Comput Chem , vol.2 , pp. 287-303
    • Weiner, P.1    Kollman, P.2
  • 20
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FlexX incremental construction algorithm for protein-ligand docking
    • Kramer B, Rarey M, Lengauer T (1999) Evaluation of the FlexX incremental construction algorithm for protein-ligand docking. Proteins: Structure, Function, and Genetics 37:228-241.
    • (1999) Proteins: Structure, Function, and Genetics , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 21
    • 0041919542 scopus 로고    scopus 로고
    • Improved protein-ligand docking using GOLD
    • Verdonk M et al (2003) Improved protein-ligand docking using GOLD. Proteins 52:609-623.
    • (2003) Proteins , vol.52 , pp. 609-623
    • Verdonk, M.1
  • 22
    • 0035011980 scopus 로고    scopus 로고
    • Protein ligand docking based on empirical method for binding affinity estimation
    • Tao P, Lai L (2001) Protein ligand docking based on empirical method for binding affinity estimation. J Comput Aided Mol Des 15:429-446.
    • (2001) J Comput Aided Mol des , vol.15 , pp. 429-446
    • Tao, P.1    Lai, L.2
  • 23
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang RX, Lai LH, Wang SM (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16:11-26.
    • (2002) J Comput Aided Mol des , vol.16 , pp. 11-26
    • Wang, R.X.1    Lai, L.H.2    Wang, S.M.3
  • 24
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam CM, Jiang X, Oldfield T, Waldman M (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 21:289-307.
    • (2003) J Mol Graph Model , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 25
    • 0035342434 scopus 로고    scopus 로고
    • High throughput docking for library design and library prioritization
    • Diller DJ, Merz KM (2001) High throughput docking for library design and library prioritization. Proteins: Structure, Function, and Genetics 43:113-124.
    • (2001) Proteins: Structure, Function, and Genetics , vol.43 , pp. 113-124
    • Diller, D.J.1    Merz, K.M.2
  • 26
    • 0030598347 scopus 로고    scopus 로고
    • Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
    • Meyer M, Wilson P, Schomburg D (1996) Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J Mol Biol 264:199-210.
    • (1996) J Mol Biol , vol.264 , pp. 199-210
    • Meyer, M.1    Wilson, P.2    Schomburg, D.3
  • 27
    • 33644843080 scopus 로고    scopus 로고
    • PSI-DOCK: towards highly efficient and accurate flexible ligand docking
    • Pei JF et al (2006) PSI-DOCK: towards highly efficient and accurate flexible ligand docking. Proteins: Structure, Function, and Bioinformatics 62:934-946.
    • (2006) Proteins: Structure, Function, and Bioinformatics , vol.62 , pp. 934-946
    • Pei, J.F.1
  • 28
    • 0013133162 scopus 로고    scopus 로고
    • A new test set for validating predictions of protein-ligand interaction
    • Nissink JWM et al (2002) A new test set for validating predictions of protein-ligand interaction. Proteins: Structure, Function, and Genetics 49:457-471.
    • (2002) Proteins: Structure, Function, and Genetics , vol.49 , pp. 457-471
    • Nissink, J.W.M.1
  • 30
    • 77954761386 scopus 로고
    • Tripos Inc, South Hanley Rd, St Louis, Missouri 63144, USA
    • SYBYL, Tripos Inc, 1699 South Hanley Rd, St Louis, Missouri 63144, USA.
    • (1699) SYBYL
  • 31
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang RX, Lu YP, Wang SM (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46:2287-2303.
    • (2003) J Med Chem , vol.46 , pp. 2287-2303
    • Wang, R.X.1    Lu, Y.P.2    Wang, S.M.3
  • 32
    • 84975562075 scopus 로고
    • Closed-form solution of absolute orientation using orthonormal matrices
    • Horn B, Hilden H, Negahdaripour S (1988) Closed-form solution of absolute orientation using orthonormal matrices. J Opt Soc Am A 5:1127-1135.
    • (1988) J Opt Soc Am A , vol.5 , pp. 1127-1135
    • Horn, B.1    Hilden, H.2    Negahdaripour, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.