메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

Author keywords

[No Author keywords available]

Indexed keywords

BIOACTIVE CONFORMATION; COMPARATIVE ANALYSIS; CONFORMATIONAL ENERGIES; CONFORMATIONAL ENSEMBLE; CONFORMATIONAL SAMPLINGS; DRUG DISCOVERY RESEARCHES; FORCE FIELD BASED METHODS; MULTI-OBJECTIVE EVOLUTION ALGORITHMS;

EID: 78049408261     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-545     Document Type: Article
Times cited : (28)

References (38)
  • 1
    • 65949087682 scopus 로고    scopus 로고
    • TCONCOORD-GUI: visually supported conformational sampling of bioactive molecules
    • 10.1002/jcc.21127, 18942729
    • Seeliger D, Groot BD. tCONCOORD-GUI: visually supported conformational sampling of bioactive molecules. J Comput Chem 2009, 30:1160-6. 10.1002/jcc.21127, 18942729.
    • (2009) J Comput Chem , vol.30 , pp. 1160-1166
    • Seeliger, D.1    Groot, B.D.2
  • 2
    • 65549133951 scopus 로고    scopus 로고
    • Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation
    • 10.1186/1471-2105-10-101, 2678094, 19335906
    • Liu X, Bai F, Ouyang S, Wang X, Li H, Jiang H. Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. BMC Bioinformatics 2009, 10:101. 10.1186/1471-2105-10-101, 2678094, 19335906.
    • (2009) BMC Bioinformatics , vol.10 , pp. 101
    • Liu, X.1    Bai, F.2    Ouyang, S.3    Wang, X.4    Li, H.5    Jiang, H.6
  • 3
    • 0029444383 scopus 로고
    • A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
    • Jones G, Willett P, Glen RC. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J Comput Aided-Mol 1995, 9:532-549.
    • (1995) J Comput Aided-Mol , vol.9 , pp. 532-549
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 4
    • 67650097333 scopus 로고    scopus 로고
    • Novel Method for the Evaluation of 3D Conformation Generators
    • 10.1021/ci800393w, 19435329
    • Takagi T, Amano M, Tomimoto M. Novel Method for the Evaluation of 3D Conformation Generators. J Chem Inf Model 2009, 49:1377-1388. 10.1021/ci800393w, 19435329.
    • (2009) J Chem Inf Model , vol.49 , pp. 1377-1388
    • Takagi, T.1    Amano, M.2    Tomimoto, M.3
  • 5
    • 37249065124 scopus 로고    scopus 로고
    • Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm
    • 10.1021/ci6005646, 17892278
    • Vainio MJ, Johnson MS. Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm. J Chem Inf Model 2007, 47:2462-2474. 10.1021/ci6005646, 17892278.
    • (2007) J Chem Inf Model , vol.47 , pp. 2462-2474
    • Vainio, M.J.1    Johnson, M.S.2
  • 6
    • 28944441241 scopus 로고    scopus 로고
    • McQSAR: A Multiconformational Quantitative Structure activity Relationship Engine Driven by Genetic Algorithms
    • 10.1021/ci0501847, 16309302
    • Vainio MJ, Johnson MS. McQSAR: A Multiconformational Quantitative Structure activity Relationship Engine Driven by Genetic Algorithms. J Chem Inf Model 2005, 45:1953-1961. 10.1021/ci0501847, 16309302.
    • (2005) J Chem Inf Model , vol.45 , pp. 1953-1961
    • Vainio, M.J.1    Johnson, M.S.2
  • 7
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: methods and applications
    • 10.1038/nrd1549, 15520816
    • Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 2004, 3:935-949. 10.1038/nrd1549, 15520816.
    • (2004) Nat Rev Drug Discov , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 8
    • 0036835460 scopus 로고    scopus 로고
    • Integration of virtual and high-throughput screening
    • 10.1038/nrd941, 12415248
    • Bajorath J. Integration of virtual and high-throughput screening. Nat Rev Drug Discov 2002, 1:882-894. 10.1038/nrd941, 12415248.
    • (2002) Nat Rev Drug Discov , vol.1 , pp. 882-894
    • Bajorath, J.1
  • 10
    • 61349109390 scopus 로고    scopus 로고
    • MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space
    • 10.1016/j.ejmech.2008.09.052, 19022539
    • Sperandio O, Souaille M, Delfaud F, Miteva MA, Villoutreix BO. MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. Eur J Med Chem 2008, 44:1405-1409. 10.1016/j.ejmech.2008.09.052, 19022539.
    • (2008) Eur J Med Chem , vol.44 , pp. 1405-1409
    • Sperandio, O.1    Souaille, M.2    Delfaud, F.3    Miteva, M.A.4    Villoutreix, B.O.5
  • 11
    • 54249157493 scopus 로고    scopus 로고
    • Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns
    • 10.1021/ci8001793, 18698838
    • Auer J, Bajorath. Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns. J Chem Inf Model 2008, 48:1747-1753. 10.1021/ci8001793, 18698838.
    • (2008) J Chem Inf Model , vol.48 , pp. 1747-1753
    • Auer, J.1    Bajorath2
  • 12
    • 23644462571 scopus 로고    scopus 로고
    • A new conformational search technique and its applications
    • Vengadesan K, Gautham N. A new conformational search technique and its applications. Curr Sci 2005, 88:1759-1770.
    • (2005) Curr Sci , vol.88 , pp. 1759-1770
    • Vengadesan, K.1    Gautham, N.2
  • 13
    • 0000782536 scopus 로고    scopus 로고
    • A new approach to probing conformational space with molecular mechanics: random incremental pulse search
    • Ferguson DM, Raber DJ. A new approach to probing conformational space with molecular mechanics: random incremental pulse search. J Am Chem Soc 2002, 111:4371-4378.
    • (2002) J Am Chem Soc , vol.111 , pp. 4371-4378
    • Ferguson, D.M.1    Raber, D.J.2
  • 14
    • 77951987154 scopus 로고    scopus 로고
    • ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
    • 10.1021/ci100015j, 20373803
    • Watts KS, Dalal P, Murphy RB, Sherman W, Friesner RA, Shelley JC. ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. J Chem Inf Model 2010, 50:534-546. 10.1021/ci100015j, 20373803.
    • (2010) J Chem Inf Model , vol.50 , pp. 534-546
    • Watts, K.S.1    Dalal, P.2    Murphy, R.B.3    Sherman, W.4    Friesner, R.A.5    Shelley, J.C.6
  • 15
    • 35248863951 scopus 로고    scopus 로고
    • CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration
    • 10.1021/ci700136x, 17691764
    • Li J, Ehlers T, Sutter J, Varma-O'Brien S, Kirchmair J. CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration. J Chem Inf Model 2007, 47:1923-1932. 10.1021/ci700136x, 17691764.
    • (2007) J Chem Inf Model , vol.47 , pp. 1923-1932
    • Li, J.1    Ehlers, T.2    Sutter, J.3    Varma-O'Brien, S.4    Kirchmair, J.5
  • 16
    • 77951986384 scopus 로고    scopus 로고
    • Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
    • 10.1021/ci100031x, 2859685, 20235588
    • Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, Stahl MT. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model 2010, 50:572-584. 10.1021/ci100031x, 2859685, 20235588.
    • (2010) J Chem Inf Model , vol.50 , pp. 572-584
    • Hawkins, P.C.D.1    Skillman, A.G.2    Warren, G.L.3    Ellingson, B.A.4    Stahl, M.T.5
  • 17
    • 72749127604 scopus 로고    scopus 로고
    • DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening
    • 10.1186/1472-6769-9-6, 2781789, 19912625
    • Lagorce D, Pencheva T, Villoutreix B, Miteva M. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening. BMC Chem Biol 2009, 9:6. 10.1186/1472-6769-9-6, 2781789, 19912625.
    • (2009) BMC Chem Biol , vol.9 , pp. 6
    • Lagorce, D.1    Pencheva, T.2    Villoutreix, B.3    Miteva, M.4
  • 18
    • 0023173201 scopus 로고
    • Prediction of the folding of short polypeptide segments by uniform conformational sampling
    • 10.1002/bip.360260114, 3801593
    • Robert EB, Martin K. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987, 26:137-168. 10.1002/bip.360260114, 3801593.
    • (1987) Biopolymers , vol.26 , pp. 137-168
    • Robert, E.B.1    Martin, K.2
  • 19
    • 84988075077 scopus 로고
    • The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space
    • Mark L, Still WC. The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space. J Comput Chem 1988, 9:343-355.
    • (1988) J Comput Chem , vol.9 , pp. 343-355
    • Mark, L.1    Still, W.C.2
  • 20
    • 78649496395 scopus 로고    scopus 로고
    • Santa Fe, NM, U.S.A, OMEGA, OpenEye Science Software
    • OMEGA, OpenEye Science Software 2004, Santa Fe, NM, U.S.A, OMEGA, OpenEye Science Software.
    • (2004)
  • 21
    • 0037439857 scopus 로고    scopus 로고
    • Conformational analysis by intersection: CONAN
    • 10.1002/jcc.10175, 12483671
    • Smellie A, Stanton R, Henne R, Teig S. Conformational analysis by intersection: CONAN. J Comput Chem 2003, 24:10-20. 10.1002/jcc.10175, 12483671.
    • (2003) J Comput Chem , vol.24 , pp. 10-20
    • Smellie, A.1    Stanton, R.2    Henne, R.3    Teig, S.4
  • 23
    • 0035889784 scopus 로고    scopus 로고
    • Efficient exploration of conformational space using the stochastic search method: application to beta-peptide oligomers
    • Jayaraman C, Martin S, William LJ. Efficient exploration of conformational space using the stochastic search method: application to beta-peptide oligomers. J Comput Chem 2001, 22:1646-1654.
    • (2001) J Comput Chem , vol.22 , pp. 1646-1654
    • Jayaraman, C.1    Martin, S.2    William, L.J.3
  • 24
    • 27844498431 scopus 로고    scopus 로고
    • Application of torsion angle molecular dynamics for efficient sampling of protein conformations
    • 10.1002/jcc.20293, 16145655
    • Jianhan C, Wonpil I, Charles LB. Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem 2005, 26:1565-1578. 10.1002/jcc.20293, 16145655.
    • (2005) J Comput Chem , vol.26 , pp. 1565-1578
    • Jianhan, C.1    Wonpil, I.2    Charles, L.B.3
  • 25
    • 0029025224 scopus 로고
    • Conformational changes of small molecules binding to proteins
    • 10.1016/0968-0896(95)00031-B, 8581425
    • Nicklaus MC, Wang S, Driscoll JS, Milne GWA. Conformational changes of small molecules binding to proteins. Bioorg Med Chem 1995, 3:411-428. 10.1016/0968-0896(95)00031-B, 8581425.
    • (1995) Bioorg Med Chem , vol.3 , pp. 411-428
    • Nicklaus, M.C.1    Wang, S.2    Driscoll, J.S.3    Milne, G.W.A.4
  • 26
    • 0032112610 scopus 로고    scopus 로고
    • Conformational energy penalties of protein-bound ligands
    • 10.1023/A:1008007507641, 9777496
    • Boström J, Norrby P-O, Liljefors T. Conformational energy penalties of protein-bound ligands. J Comput Aided-Mol Des 1998, 12:383-383. 10.1023/A:1008007507641, 9777496.
    • (1998) J Comput Aided-Mol Des , vol.12 , pp. 383-383
    • Boström, J.1    Norrby, P.-O.2    Liljefors, T.3
  • 27
    • 2342586724 scopus 로고    scopus 로고
    • Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
    • 10.1021/jm030563w, 15115393
    • Perola E, Charifson PS. Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding. J Med Chem 2004, 47:2499-2510. 10.1021/jm030563w, 15115393.
    • (2004) J Med Chem , vol.47 , pp. 2499-2510
    • Perola, E.1    Charifson, P.S.2
  • 28
    • 0028522365 scopus 로고
    • A fast and efficient method to generate biologically relevant conformations
    • 10.1007/BF00123667, 7876902
    • Mietzner T, et al. A fast and efficient method to generate biologically relevant conformations. J Comput Aided-Mol Des 1994, 8:583-606. 10.1007/BF00123667, 7876902.
    • (1994) J Comput Aided-Mol Des , vol.8 , pp. 583-606
    • Mietzner, T.1
  • 29
    • 0004151408 scopus 로고
    • Molecular Mechanics
    • ACS Monograph No 177, Washington, DC, American Chemical Society
    • Burkert U, Allinger NL. Molecular Mechanics. 1982, ACS Monograph No 177, Washington, DC, American Chemical Society.
    • (1982)
    • Burkert, U.1    Allinger, N.L.2
  • 30
    • 84986522856 scopus 로고
    • Poling: Promoting conformational variation
    • Andrew S, Steven LT, Peter T. Poling: Promoting conformational variation. J Comput Chem 1995, 16:171-187.
    • (1995) J Comput Chem , vol.16 , pp. 171-187
    • Andrew, S.1    Steven, L.T.2    Peter, T.3
  • 31
    • 85052604127 scopus 로고    scopus 로고
    • Molecular mechanical force fields
    • Stanford University
    • Varma CK. Molecular mechanical force fields. Biochemistry 218 2001, Stanford University.
    • (2001) Biochemistry 218
    • Varma, C.K.1
  • 32
    • 31444452744 scopus 로고
    • Automatic generation of 3D-atomic coordinates for organic molecules
    • Gasteiger J, Rudolph C, Sadowski J. Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comp Method 1990, 3:537-547.
    • (1990) Tetrahedron Comp Method , vol.3 , pp. 537-547
    • Gasteiger, J.1    Rudolph, C.2    Sadowski, J.3
  • 33
    • 0036715683 scopus 로고    scopus 로고
    • Combining convergence and diversity in evolutionary multiobjective optimization
    • 10.1162/106365602760234108, 12227996
    • Marco L, Lothar T, Kalyanmoy D, Eckart Z. Combining convergence and diversity in evolutionary multiobjective optimization. Evol Comput 2002, 10:263-282. 10.1162/106365602760234108, 12227996.
    • (2002) Evol Comput , vol.10 , pp. 263-282
    • Marco, L.1    Lothar, T.2    Kalyanmoy, D.3    Eckart, Z.4
  • 34
    • 0035555863 scopus 로고    scopus 로고
    • Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
    • Boström J. Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools. J Comput Aided-Mol 2001, 15:1137-1152.
    • (2001) J Comput Aided-Mol , vol.15 , pp. 1137-1152
    • Boström, J.1
  • 35
    • 33746921247 scopus 로고    scopus 로고
    • Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations
    • 10.1021/ci060084g, 16859316
    • Kirchmair J, Wolber G, Laggner C, Langer T. Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations. J Chem Inf Model 2006, 46:1848-1861. 10.1021/ci060084g, 16859316.
    • (2006) J Chem Inf Model , vol.46 , pp. 1848-1861
    • Kirchmair, J.1    Wolber, G.2    Laggner, C.3    Langer, T.4
  • 36
    • 0142236572 scopus 로고    scopus 로고
    • Low Mode Search. An Efficient, Automated Computational Method for Conformational Analysis: Application to Cyclic and Acyclic Alkanes and Cyclic Peptides
    • Kolossváry I, Guida WC. Low Mode Search. An Efficient, Automated Computational Method for Conformational Analysis: Application to Cyclic and Acyclic Alkanes and Cyclic Peptides. J Am Chem Soc 1996, 118:5011-5019.
    • (1996) J Am Chem Soc , vol.118 , pp. 5011-5019
    • Kolossváry, I.1    Guida, W.C.2
  • 37
    • 0043162336 scopus 로고
    • An internal-coordinate Monte Carlo method for searching conformational space
    • Chang G, Guida WC, Still WC. An internal-coordinate Monte Carlo method for searching conformational space. J Am Chem Soc 1989, 111:4379-4386.
    • (1989) J Am Chem Soc , vol.111 , pp. 4379-4386
    • Chang, G.1    Guida, W.C.2    Still, W.C.3
  • 38
    • 73349120955 scopus 로고    scopus 로고
    • Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use
    • 10.1021/ci9001926, 19919051
    • Tresadern G, Agrafiotis DK. Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use. J Chem Inf Model 2009, 49:2786-2800. 10.1021/ci9001926, 19919051.
    • (2009) J Chem Inf Model , vol.49 , pp. 2786-2800
    • Tresadern, G.1    Agrafiotis, D.K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.