메뉴 건너뛰기




Volumn 51, Issue 4, 2011, Pages 897-908

Short nonbonded contact distances in organic molecules and their use as atom-clash criteria in conformer validation and searching

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; CRYSTAL ATOMIC STRUCTURE; HYDROGEN BONDS; MOLECULAR MODELING; MOLECULES; VAN DER WAALS FORCES;

EID: 79955390825     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100466h     Document Type: Article
Times cited : (10)

References (32)
  • 1
    • 77249106566 scopus 로고    scopus 로고
    • Three-Dimensional Pharmacophore Methods in Drug Discovery
    • Leach, A. R.; Gillet, V. J.; Lewis, R. A.; Taylor, R. Three-Dimensional Pharmacophore Methods in Drug Discovery J. Med. Chem. 2010, 53, 539-558
    • (2010) J. Med. Chem. , vol.53 , pp. 539-558
    • Leach, A.R.1    Gillet, V.J.2    Lewis, R.A.3    Taylor, R.4
  • 4
    • 50249126705 scopus 로고    scopus 로고
    • A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
    • Dorfman, R. J.; Smith, K. M.; Masek, B. B.; Clark, R. D. A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers J. Comput.-Aided Mol. Des. 2008, 22, 681-691
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 681-691
    • Dorfman, R.J.1    Smith, K.M.2    Masek, B.B.3    Clark, R.D.4
  • 5
    • 70350501158 scopus 로고    scopus 로고
    • Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size
    • Griewel, A.; Kayser, O.; Schlosser, J.; Rarey, M. Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size J. Chem. Inf. Model. 2009, 49, 2203-2311
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2203-2311
    • Griewel, A.1    Kayser, O.2    Schlosser, J.3    Rarey, M.4
  • 6
    • 77951986384 scopus 로고    scopus 로고
    • Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
    • Hawkins, P. C. D.; Skillman, A. G.; Warren, G. L.; Ellingson, B. A.; Stahl, M. T. 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
    • (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
  • 7
    • 35248863951 scopus 로고    scopus 로고
    • CAESAR: A new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration
    • DOI 10.1021/ci700136x
    • 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 (Pubitemid 47561140)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.5 , pp. 1923-1932
    • Li, J.1    Ehlers, T.2    Sutter, J.3    Varma-O'Brien, S.4    Kirchmair, J.5
  • 10
    • 37249065124 scopus 로고    scopus 로고
    • Generating conformer ensembles using a multiobjective genetic algorithm
    • DOI 10.1021/Ci6005646
    • Vainio, M. J.; Johnson, M. Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm J. Chem. Inf. Model. 2007, 47, 2462-2474 (Pubitemid 350275111)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.6 , pp. 2462-2474
    • Vainio, M.J.1    Johnson, M.S.2
  • 12
    • 34247509773 scopus 로고    scopus 로고
    • Self-organizing superimposition algorithm for conformational sampling
    • DOI 10.1002/jcc.20622
    • Zhu, F.; Agrafiotis, D. K. Self-Organising Superimposition Algorithm for Conformational Sampling J. Comput. Chem. 2007, 28, 1234-1239 (Pubitemid 46652997)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.7 , pp. 1234-1239
    • Zhu, F.1    Agrafiotis, D.K.2
  • 13
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • DOI 10.1107/S0108768102003890
    • Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising Acta Crystallogr., Sect. B: Struct. Sci. 2002, 58, 380-388 (Pubitemid 135702674)
    • (2002) Acta Crystallographica Section B: Structural Science , vol.58 , Issue.3 PART 1 , pp. 380-388
    • Allen, F.H.1
  • 14
    • 0028466540 scopus 로고
    • Comparison of automatic three-dimensional model builders using 639 X-ray structures
    • Sadowski, J.; Gasteiger, J.; Klebe, G. Comparison of automatic three-dimensional model builders using 639 X-ray structures J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008
    • (1994) J. Chem. Inf. Comput. Sci. , vol.34 , pp. 1000-1008
    • Sadowski, J.1    Gasteiger, J.2    Klebe, G.3
  • 15
    • 84988115618 scopus 로고
    • Validation of the General Purpose Tripos 5.2 Force Field
    • Clark, M.; Cramer, R. D., III; Van Opdenbosch, N. Validation of the General Purpose Tripos 5.2 Force Field J. Comput. Chem. 1989, 10, 982-1012
    • (1989) J. Comput. Chem. , vol.10 , pp. 982-1012
    • Clark, M.1    Cramer III, R.D.2    Van Opdenbosch, N.3
  • 16
    • 0347296066 scopus 로고    scopus 로고
    • Assessing the performance of OMEGA with respect to retrieving bioactive conformations
    • DOI 10.1016/S1093-3263(02)00204-8, PII S1093326302002048
    • Boström, J.; Greenwood, J. R.; Gottfries, J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations J. Mol. Graphics Modell. 2003, 21, 449-462 (Pubitemid 36120775)
    • (2003) Journal of Molecular Graphics and Modelling , vol.21 , Issue.5 , pp. 449-462
    • Bostrom, J.1    Greenwood, J.R.2    Gottfries, J.3
  • 17
    • 0036022976 scopus 로고    scopus 로고
    • Can we separate active from inactive conformations?
    • DOI 10.1023/A:1016320106741
    • Diller, D. J.; Merz, J. M., Jr. Can we separate active from inactive conformations? J. Comput.-Aided Mol. Des. 2002, 16, 105-112 (Pubitemid 34855037)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.2 , pp. 105-112
    • Diller, D.J.1    Merz Jr., K.M.2
  • 19
    • 2342586724 scopus 로고    scopus 로고
    • Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
    • DOI 10.1021/jm030563w
    • Perola, E.; Charifson, P. S. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganisation upon binding J. Med. Chem. 2004, 47, 2499-2510 (Pubitemid 38580088)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.10 , pp. 2499-2510
    • Perola, E.1    Charifson, P.S.2
  • 20
    • 77952750760 scopus 로고    scopus 로고
    • Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst
    • Chen, I.-J.; Foloppe, N. Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst J. Chem. Inf. Model. 2010, 50, 822-839
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 822-839
    • Chen, I.-J.1    Foloppe, N.2
  • 21
    • 77952836900 scopus 로고    scopus 로고
    • Bond lengths in organic and metal-organic compounds revisited: X-H bond lengths from neutron diffraction data
    • Allen, F. H.; Bruno, I. J. Bond lengths in organic and metal-organic compounds revisited: X-H bond lengths from neutron diffraction data Acta Crystallogr., Sect. B: Struct. Sci. 2010, 66, 380-386
    • (2010) Acta Crystallogr., Sect. B: Struct. Sci. , vol.66 , pp. 380-386
    • Allen, F.H.1    Bruno, I.J.2
  • 23
    • 20544433165 scopus 로고
    • Van der Waals Volumes and Radii
    • Bondi, A. Van der Waals Volumes and Radii J. Phys. Chem. 1964, 68, 441-451
    • (1964) J. Phys. Chem. , vol.68 , pp. 441-451
    • Bondi, A.1
  • 24
    • 33748546968 scopus 로고    scopus 로고
    • Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals Radii
    • Rowland, R. S.; Taylor, R. Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii J. Phys. Chem. 1996, 100, 7384-7391 (Pubitemid 126789411)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.18 , pp. 7384-7391
    • Rowland, R.S.1    Taylor, R.2
  • 25
    • 0026772847 scopus 로고
    • Computational Studies of Nonbonded Sulfur-Oxygen and Selenium-Oxygen Interactions in the Thiazole and Selenazole Nucleosides
    • Burling, F. T.; Goldstein, B. M. Computational Studies of Nonbonded Sulfur-Oxygen and Selenium-Oxygen Interactions in the Thiazole and Selenazole Nucleosides J. Am. Chem. Soc. 1992, 114, 2313-2320
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 2313-2320
    • Burling, F.T.1    Goldstein, B.M.2
  • 26
    • 0000954249 scopus 로고
    • A Database Study of Nonbonded Intramolecular Sulfur-Nucleophile Contacts
    • Burling, F. T.; Goldstein, B. M. A Database Study of Nonbonded Intramolecular Sulfur-Nucleophile Contacts Acta Crystallogr., Sect. B: Struct. Sci. 1993, 49, 738-744
    • (1993) Acta Crystallogr., Sect. B: Struct. Sci. , vol.49 , pp. 738-744
    • Burling, F.T.1    Goldstein, B.M.2
  • 28
    • 37249023634 scopus 로고    scopus 로고
    • Torsion angle preference and energetics of small-molecule ligands bound to proteins
    • DOI 10.1021/ci700189s
    • Hao, M.-H.; Haq, O.; Muegge, I. Torsion Angle Preference and Energetics of Small-Molecule Ligands Bound to Proteins J. Chem. Inf. Model. 2007, 47, 2242-2252 (Pubitemid 350275089)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.6 , pp. 2242-2252
    • Hao, M.-H.1    Haq, O.2    Muegge, I.3
  • 29
    • 60749137646 scopus 로고    scopus 로고
    • Toward accurate relative energy predictions of the bioactive conformation of drugs
    • Butler, K. T.; Luque, F. J.; Barril, X. Toward accurate relative energy predictions of the bioactive conformation of drugs J. Comput. Chem. 2009, 30, 601-610
    • (2009) J. Comput. Chem. , vol.30 , pp. 601-610
    • Butler, K.T.1    Luque, F.J.2    Barril, X.3
  • 31
    • 39449105474 scopus 로고    scopus 로고
    • Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis
    • DOI 10.1021/ci7002494
    • Brameld, K. A.; Kuhn, B.; Reuter, D. C.; Stahl, M. Small Molecule Conformational Preferences from Crystal Structure Data. A Medicinal Chemistry Focused Analysis J. Chem. Inf. Model. 2008, 48, 1-24 (Pubitemid 351271046)
    • (2008) Journal of Chemical Information and Modeling , vol.48 , Issue.1 , pp. 1-24
    • Brameld, K.A.1    Kuhn, B.2    Reuter, D.C.3    Stahl, M.4
  • 32
    • 33845786627 scopus 로고    scopus 로고
    • MIMUMBA revisited: Torsion angle rules for conformer generation derived from X-ray structures
    • DOI 10.1021/ci060042s
    • Sadowski, J.; Boström, J. MIMUMBA Revisited: Torsion Angle Rules for Conformer Generation Derived from X-Ray Structures J. Chem. Inf. Model. 2006, 46, 2305-2309 (Pubitemid 46008104)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2305-2309
    • Sadowski, J.1    Bostrom, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.