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Volumn 25, Issue 8, 2011, Pages 777-783

Open3DALIGN: An open-source software aimed at unsupervised ligand alignment

Author keywords

Alignment; Cheminformatics; Pharmacophore; Superposition

Indexed keywords

ALIGNMENT; OPEN SYSTEMS; PHARMACODYNAMICS;

EID: 80055090579     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9462-9     Document Type: Article
Times cited : (116)

References (24)
  • 1
    • 77957222179 scopus 로고    scopus 로고
    • Training a scoring function for the alignment of small molecules
    • Chan SL, Labute P (2010) Training a scoring function for the alignment of small molecules. J Chem Inf Model 50:1724-1735
    • (2010) J Chem Inf Model , vol.50 , pp. 1724-1735
    • Chan, S.L.1    Labute, P.2
  • 2
    • 0034065350 scopus 로고    scopus 로고
    • Computational methods for the structural alignment of molecules
    • DOI 10.1023/A:1008194019144
    • Lemmen C, Lengauer T (2000) Computational methods for the structural alignment of molecules. J Comput Aided Mol Des 14:215-232 (Pubitemid 30175941)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.3 , pp. 215-232
    • Lemmen, C.1    Lengauer, T.2
  • 3
    • 77249106566 scopus 로고    scopus 로고
    • Three-dimensional pharmacophore methods in drug discovery
    • Leach AR, Gillet VJ, Lewis RA, Taylor R (2010) Three-dimensional pharmacophore methods in drug discovery. J Med Chem 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
    • 33748250857 scopus 로고    scopus 로고
    • BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization
    • DOI 10.1007/s10822-006-9052-4
    • Rönkkö T, Tervo AJ, Parkkinen J, Poso A (2006) BRUTUS: optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization. J Comput Aided Mol Des 20:227-236 (Pubitemid 44317515)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.4 , pp. 227-236
    • Rokko, T.1    Tervo, A.J.2    Parkkinen, J.3    Poso, A.4
  • 5
    • 65249167560 scopus 로고    scopus 로고
    • ShaEP: Molecular overlay based on shape and electrostatic potential
    • Vainio MJ, Santeri Puranen J, Johnson MS (2009) ShaEP: molecular overlay based on shape and electrostatic potential. J Chem Inf Model 49:492-502
    • (2009) J Chem Inf Model , vol.49 , pp. 492-502
    • Vainio, M.J.1    Santeri Puranen, J.2    Johnson, M.S.3
  • 6
    • 5644236834 scopus 로고    scopus 로고
    • Pharmacophore modeling and three dimensional database searching for drug design using catalyst: Recent advances
    • Güner O, Clement O, Kurogi Y (2004) Pharmacophore modeling and three dimensional database searching for drug design using Catalyst: recent advances. Curr Med Chem 11:2991-3005 (Pubitemid 39369268)
    • (2004) Current Medicinal Chemistry , vol.11 , Issue.22 , pp. 2991-3005
    • Guner, O.1    Clement, O.2    Kurogi, Y.3
  • 7
    • 33845868822 scopus 로고    scopus 로고
    • PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
    • DOI 10.1007/s10822-006-9087-6
    • Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA (2006) PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 20:647-671 (Pubitemid 46023928)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.10-11 , pp. 647-671
    • Dixon, S.L.1    Smondyrev, A.M.2    Knoll, E.H.3    Rao, S.N.4    Shaw, D.E.5    Friesner, R.A.6
  • 9
    • 78650755036 scopus 로고    scopus 로고
    • History of 3D pharmacophore searching: Commercial, academic and open-source tools
    • Van Drie JH (2010) History of 3D pharmacophore searching: commercial, academic and open-source tools. Drug Disc Today 7:e255-e262
    • (2010) Drug Disc Today , vol.7
    • Van Drie, J.H.1
  • 10
    • 52049125711 scopus 로고    scopus 로고
    • Pharao: Pharmacophore alignment and optimization
    • Taminau J, Thijs G, De Winter H (2008) Pharao: pharmacophore alignment and optimization. J Mol Graph Model 27:161-169
    • (2008) J Mol Graph Model , vol.27 , pp. 161-169
    • Taminau, J.1    Thijs, G.2    De Winter, H.3
  • 11
    • 33745135773 scopus 로고    scopus 로고
    • Recent developments of the Chemistry Development Kit (CDK) - An open-source Java library for chemo- and bioinformatics
    • DOI 10.2174/138161206777585274
    • Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL (2006) Recent developments of the chemistry development kit (CDK)-an open-source java library for chemo- and bioinformatics. Curr Pharm Des 12:2111-2120 (Pubitemid 43891407)
    • (2006) Current Pharmaceutical Design , vol.12 , Issue.17 , pp. 2111-2120
    • Steinbeck, C.1    Hoppe, C.2    Kuhn, S.3    Floris, M.4    Guha, R.5    Willighagen, E.L.6
  • 13
    • 78651426971 scopus 로고    scopus 로고
    • Open3DQSAR: A new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields
    • Accessed 13 June 2011
    • Tosco P, Balle T (2011) Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields. J Mol Model 17: 201-208; http:// open3dqsar.org/. Accessed 13 June 2011
    • (2011) J Mol Model , vol.17 , pp. 201-208
    • Tosco, P.1    Balle, T.2
  • 14
    • 0026752259 scopus 로고
    • Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogs
    • O'Connor SD, Smith PE, al-Obeidi F, Pettitt BM (1992) Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogs. J Med Chem 35:2870-2881
    • (1992) J Med Chem , vol.35 , pp. 2870-2881
    • O'Connor, S.D.1    Smith, P.E.2    Al-Obeidi, F.3    Pettitt, B.M.4
  • 16
    • 80255123469 scopus 로고    scopus 로고
    • SDF2XYZ2SDF: How to exploit TINKER power in chemoinformatics projects
    • Doi: 1007/s00894-011-1111-7 Accessed 13 June 2011
    • Tosco P, Balle T, Shiri F (2011) SDF2XYZ2SDF: how to exploit TINKER power in chemoinformatics projects. J Mol Model. Doi: 1007/s00894-011-1111-7; http://sdf2xyz2sdf.sourceforge.net/. Accessed 13 June 2011
    • (2011) J Mol Model
    • Tosco, P.1    Balle, T.2    Shiri, F.3
  • 18
    • 80055064743 scopus 로고    scopus 로고
    • MOE 2010.10; Chemical Computing Group Inc., Montreal, Quebec, Canada, 2010
    • MOE 2010.10; Chemical Computing Group Inc., Montreal, Quebec, Canada, 2010
  • 19
    • 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
    • DOI 10.1021/ci060084g
    • Kirchmair J, Wolber G, Laggner C, Langer T (2006) 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 46:1848-1861 (Pubitemid 44185709)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.4 , pp. 1848-1861
    • Kirchmair, J.1    Wolber, G.2    Laggner, C.3    Langer, T.4
  • 20
    • 4444343398 scopus 로고    scopus 로고
    • Alignment of three-dimensional molecules using an image recognition algorithm
    • DOI 10.1016/j.jmgm.2004.04.004, PII S1093326304000592
    • Richmond NJ, Willett P, Clark RD (2004) Alignment of threedimensional molecules using an image recognition algorithm. J Mol Graph Model 23:199-209 (Pubitemid 39195288)
    • (2004) Journal of Molecular Graphics and Modelling , vol.23 , Issue.2 , pp. 199-209
    • Richmond, N.J.1    Willett, P.2    Clark, R.D.3
  • 21
    • 0023173192 scopus 로고
    • Shortest augmenting path algorithm for dense and sparse linear assignment problems
    • Jonker R, Volgenant A (1987) A shortest augmenting path algorithm for dense and sparse linear assignment problems. Computing 38:325-340 (Pubitemid 17658282)
    • (1987) Computing (Vienna/New York) , vol.38 , Issue.4 , pp. 325-340
    • Volgenant, A.1    Jonker, R.2
  • 22
    • 0002404088 scopus 로고
    • On the orthogonal transformation used for structural comparisons
    • Kearsley SK (1989) On the orthogonal transformation used for structural comparisons. Acta Cryst A45:208-210
    • (1989) Acta Cryst A , vol.45 , pp. 208-210
    • Kearsley, S.K.1
  • 23
    • 0001582303 scopus 로고    scopus 로고
    • Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm
    • PII S0097848598000175
    • Petitjean M (1998) Interactive maximal common 3D substructure searching with the combined SDM/RMS algorithm. Computers Chem 22:463-465 (Pubitemid 128428280)
    • (1998) Computers and Chemistry , vol.22 , Issue.6 , pp. 463-465
    • Petitjean, M.1
  • 24
    • 6044244849 scopus 로고    scopus 로고
    • A comparison of methods for modeling quantitative structure-activity relationships
    • DOI 10.1021/jm0497141
    • Sutherland JJ, O'Brien LA, Weaver DF (2004) A comparison of methods for modeling quantitative structure-activity relationships. J Med Chem 47:5541-5554 (Pubitemid 39382801)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.22 , pp. 5541-5554
    • Sutherland, J.J.1    O'Brien, L.A.2    Weaver, D.F.3


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