메뉴 건너뛰기




Volumn 52, Issue 5, 2012, Pages 1262-1274

Potential and limitations of ensemble docking

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; LIGANDS;

EID: 84861499934     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci2005934     Document Type: Article
Times cited : (143)

References (71)
  • 2
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • Teague, S. J. Implications of protein flexibility for drug discovery Nat. Rev. Drug Discovery 2003, 2, 527-541 (Pubitemid 37361745)
    • (2003) Nature Reviews Drug Discovery , vol.2 , Issue.7 , pp. 527-541
    • Teague, S.J.1
  • 3
    • 0041989635 scopus 로고    scopus 로고
    • Conformational flexibility models for the receptor in structure based drug design
    • DOI 10.2174/1381612033454595
    • Teodoro, M. L.; Kavraki, L. E. Conformational flexibility models for the receptor in structure based drug design Curr. Pharm. Des. 2003, 9, 1635-1648 (Pubitemid 36966031)
    • (2003) Current Pharmaceutical Design , vol.9 , Issue.20 , pp. 1635-1648
    • Teodoro, M.L.1    Kavraki, L.E.2
  • 4
    • 77952724140 scopus 로고    scopus 로고
    • In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding
    • Henzler, A. M.; Rarey, M. In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding Mol. Inf. 2010, 29, 164-173
    • (2010) Mol. Inf. , vol.29 , pp. 164-173
    • Henzler, A.M.1    Rarey, M.2
  • 5
    • 63149162777 scopus 로고    scopus 로고
    • Managing protein flexibility in docking and its applications
    • B-Rao, C.; Subramanian, J.; Sharma, S. D. Managing protein flexibility in docking and its applications Drug Discovery Today 2009, 14, 394-400
    • (2009) Drug Discovery Today , vol.14 , pp. 394-400
    • B-Rao, C.1    Subramanian, J.2    Sharma, S.D.3
  • 6
    • 0001858251 scopus 로고
    • Application of a Theory of Enzyme Specificity to Protein Synthesis
    • Koshland, D. E. Application of a Theory of Enzyme Specificity to Protein Synthesis Proc. Natl. Acad. Sci. U.S.A 1958, 44, 98-104
    • (1958) Proc. Natl. Acad. Sci. U.S.A , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 7
    • 33751423377 scopus 로고    scopus 로고
    • How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding
    • DOI 10.1016/j.jmb.2006.09.062, PII S0022283606012861
    • Gunasekaran, K.; Nussinov, R. How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding J. Mol. Biol. 2007, 365, 257-273 (Pubitemid 44821204)
    • (2007) Journal of Molecular Biology , vol.365 , Issue.1 , pp. 257-273
    • Gunasekaran, K.1    Nussinov, R.2
  • 8
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • DOI 10.1016/j.jmb.2004.11.013, PII S0022283604014391
    • Gutteridge, A.; Thornton, J. Conformational changes observed in enzyme crystal structures upon substrate binding J. Mol. Biol. 2005, 346, 21-28 (Pubitemid 40128303)
    • (2005) Journal of Molecular Biology , vol.346 , Issue.1 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 9
    • 4744365803 scopus 로고    scopus 로고
    • Soft docking and multiple receptor conformations in virtual screening
    • DOI 10.1021/jm049756p
    • Ferrari, A. M.; Wei, B. Q.; Costantino, L.; Shoichet, B. K. Soft Docking and Multiple Receptor Conformations in Virtual Screening J. Med. Chem. 2004, 47, 5076-5084 (Pubitemid 39314905)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.21 , pp. 5076-5084
    • Ferrari, A.M.1    Wei, B.Q.2    Costantino, L.3    Shoichet, B.K.4
  • 10
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A. R. Ligand docking to proteins with discrete side-chain flexibility J. Mol. Biol. 1994, 235, 345-356 (Pubitemid 24049519)
    • (1994) Journal of Molecular Biology , vol.235 , Issue.1 , pp. 345-356
    • Leach, A.R.1
  • 12
    • 0042282803 scopus 로고    scopus 로고
    • FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
    • Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function J. Comput. Chem. 2003, 24, 1637-1656
    • (2003) J. Comput. Chem. , vol.24 , pp. 1637-1656
    • Taylor, R.D.1    Jewsbury, P.J.2    Essex, J.W.3
  • 13
    • 53549100784 scopus 로고    scopus 로고
    • Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening
    • Kokh, D. B.; Wenzel, W. Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening J. Med. Chem. 2008, 51, 5919-5931
    • (2008) J. Med. Chem. , vol.51 , pp. 5919-5931
    • Kokh, D.B.1    Wenzel, W.2
  • 14
    • 0037379786 scopus 로고    scopus 로고
    • Ligand-induced conformational changes: Improved predictions of ligand binding conformations and affinities
    • Frimurer, T. M.; Peters, G. H.; Iversen, L. F.; Andersen, H. S.; Møller, N. P. H; Olsen, O. H. Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities Biophys. J. 2003, 84, 2273-2281 (Pubitemid 36373550)
    • (2003) Biophysical Journal , vol.84 , Issue.4 , pp. 2273-2281
    • Frimurer, T.M.1    Peters, G.H.2    Iversen, L.F.3    Andersen, H.S.4    Moller, N.P.H.5    Olsen, O.H.6
  • 15
    • 50249132694 scopus 로고    scopus 로고
    • Protein-ligand docking with multiple flexible side chains
    • Zhao, Y.; Sanner, M. Protein-ligand docking with multiple flexible side chains J. Comput.-Aided Mol. Des. 2008, 22, 673-679
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 673-679
    • Zhao, Y.1    Sanner, M.2
  • 16
    • 27144484954 scopus 로고    scopus 로고
    • Receptor flexibility in de novo ligand design and docking
    • DOI 10.1021/jm050196j
    • Alberts, I. L.; Todorov, N. P.; Dean, P. M. Receptor Flexibility in de Novo Ligand Design and Docking J. Med. Chem. 2005, 48, 6585-6596 (Pubitemid 41504716)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.21 , pp. 6585-6596
    • Alberts, I.L.1    Todorov, N.P.2    Dean, P.M.3
  • 17
    • 0034656949 scopus 로고    scopus 로고
    • Side-chain flexibility in proteins upon ligand binding
    • DOI 10.1002/(SICI)1097-0134(20000 515)39:3<261::AID-PROT 90>3.0.CO;2-4
    • Najmanovich, R.; Kuttner, J.; Sobolev, V.; Edelman, M. Side-chain flexibility in proteins upon ligand binding Proteins: Struct., Funct., Genet. 2000, 39, 261-268 (Pubitemid 30226508)
    • (2000) Proteins: Structure, Function and Genetics , vol.39 , Issue.3 , pp. 261-268
    • Najmanovich, R.1    Kuttner, J.2    Sobolev, V.3    Edelman, M.4
  • 18
    • 0032147007 scopus 로고    scopus 로고
    • Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers
    • DOI 10.1002/(SICI)1097-0134(199 80801)32:2<159::AID-PRO T3>3.0.CO;2-G
    • Sandak, B.; Wolfson, H. J.; Nussinov, R. Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers Proteins: Struct., Funct., Genet. 1998, 32, 159-174 (Pubitemid 28363898)
    • (1998) Proteins: Structure, Function and Genetics , vol.32 , Issue.2 , pp. 159-174
    • Sandak, B.1    Wolfson, H.J.2    Nussinov, R.3
  • 21
    • 47249102090 scopus 로고    scopus 로고
    • A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
    • Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE) J. Comput.-Aided Mol. Des. 2008, 22, 311-325
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 311-325
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 23
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy
    • DOI 10.1021/jm030209y
    • Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy J. Med. Chem. 2004, 47, 45-55 (Pubitemid 38040489)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.1 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 25
    • 66149087635 scopus 로고    scopus 로고
    • Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
    • Corbeil, C. R.; Moitessier, N. Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs J. Chem. Inf. Model. 2009, 49, 997-1009
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 997-1009
    • Corbeil, C.R.1    Moitessier, N.2
  • 26
    • 67349261359 scopus 로고    scopus 로고
    • Effects of protein conformation in docking: Improved pose prediction through protein pocket adaptation
    • Jain, A. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation J. Comput.-Aided Mol. Des. 2009, 23, 355-374
    • (2009) J. Comput.-Aided Mol. Des. , vol.23 , pp. 355-374
    • Jain, A.1
  • 28
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
    • DOI 10.1023/A:1008015827877
    • Murray, C. W.; Baxter, C. A.; Frenkel, A. D. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase J. Comput.-Aided Mol. Des. 1999, 13, 547-562 (Pubitemid 29524912)
    • (1999) Journal of Computer-Aided Molecular Design , vol.13 , Issue.6 , pp. 547-562
    • Murray, C.W.1    Baxter, C.A.2    Frenkel, A.D.3
  • 29
    • 65249120827 scopus 로고    scopus 로고
    • Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
    • Rueda, M.; Bottegoni, G.; Abagyan, R. Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes J. Chem. Inf. Model. 2009, 49, 716-725
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 716-725
    • Rueda, M.1    Bottegoni, G.2    Abagyan, R.3
  • 30
    • 60549086155 scopus 로고    scopus 로고
    • Four-Dimensional Docking A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking
    • Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R. Four-Dimensional Docking A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking J. Med. Chem. 2009, 52, 397-406
    • (2009) J. Med. Chem. , vol.52 , pp. 397-406
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 31
    • 0035957528 scopus 로고    scopus 로고
    • FLEXE: Efficient molecular docking considering protein structure variations
    • DOI 10.1006/jmbi.2001.4551
    • Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: efficient molecular docking considering protein structure variations J. Mol. Biol. 2001, 308, 377-395 (Pubitemid 33043576)
    • (2001) Journal of Molecular Biology , vol.308 , Issue.2 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4
  • 33
    • 1842471241 scopus 로고    scopus 로고
    • Testing a flexible-receptor docking algorithm in a model binding site
    • DOI 10.1016/j.jmb.2004.02.015, PII S0022283604001718
    • Wei, B. Q.; Weaver, L. H.; Ferrari, A. M.; Matthews, B. W.; Shoichet, B. K. Testing a flexible-receptor docking algorithm in a model binding site J. Mol. Biol. 2004, 337, 1161-1182 (Pubitemid 38445058)
    • (2004) Journal of Molecular Biology , vol.337 , Issue.5 , pp. 1161-1182
    • Wei, B.Q.1    Weaver, L.H.2    Ferrari, A.M.3    Matthews, B.W.4    Shoichet, B.K.5
  • 34
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • DOI 10.1006/jmbi.1996.0776
    • Knegtel, R. M. A.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures J. Mol. Biol. 1997, 266, 424-440 (Pubitemid 27171024)
    • (1997) Journal of Molecular Biology , vol.266 , Issue.2 , pp. 424-440
    • Knegtel, R.M.A.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 35
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
    • DOI 10.1002/prot.21214
    • Huang, S.-Y.; Zou, X. Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking Proteins: Struct., Funct., Bioinf. 2007, 66, 399-421 (Pubitemid 46053470)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.2 , pp. 399-421
    • Huang, S.-Y.1    Zou, X.2
  • 36
    • 77951992987 scopus 로고    scopus 로고
    • Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
    • Craig, I. R.; Essex, J. W.; Spiegel, K. Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments J. Chem. Inf. Model. 2010, 50, 511-524
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 511-524
    • Craig, I.R.1    Essex, J.W.2    Spiegel, K.3
  • 37
    • 75749093371 scopus 로고    scopus 로고
    • Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
    • Rueda, M.; Bottegoni, G.; Abagyan, R. Recipes for the Selection of Experimental Protein Conformations for Virtual Screening J. Chem. Inf. Model. 2010, 50, 186-193
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 186-193
    • Rueda, M.1    Bottegoni, G.2    Abagyan, R.3
  • 39
    • 21244479779 scopus 로고    scopus 로고
    • Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
    • DOI 10.1021/jm048972v
    • Barril, X.; Morley, S. D. Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures J. Med. Chem. 2005, 48, 4432-4443 (Pubitemid 40884945)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.13 , pp. 4432-4443
    • Barril, X.1    Morley, S.D.2
  • 40
    • 34548392290 scopus 로고    scopus 로고
    • Ensemble-Docking Approach on BACE-1: Pharmacophore Perception and Guidelines for Drug Design
    • Limongelli, V.; Marinelli, L.; Cosconati, S.; Braun, H. A.; Schmidt, B.; Novellino, E. Ensemble-Docking Approach on BACE-1: Pharmacophore Perception and Guidelines for Drug Design ChemMedChem 2007, 2, 667-678
    • (2007) ChemMedChem , vol.2 , pp. 667-678
    • Limongelli, V.1    Marinelli, L.2    Cosconati, S.3    Braun, H.A.4    Schmidt, B.5    Novellino, E.6
  • 41
    • 77953325281 scopus 로고    scopus 로고
    • Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles
    • Park, S.-J.; Kufareva, I.; Abagyan, R. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles J. Comput.-Aided Mol. Des. 2010, 24, 459-471
    • (2010) J. Comput.-Aided Mol. Des. , vol.24 , pp. 459-471
    • Park, S.-J.1    Kufareva, I.2    Abagyan, R.3
  • 42
    • 34447271743 scopus 로고    scopus 로고
    • Exploring experimental sources of multiple protein conformations in structure-based drug design
    • DOI 10.1021/ja0709728
    • Damm, K. L.; Carlson, H. A. Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design J. Am. Chem. Soc. 2007, 129, 8225-8235 (Pubitemid 47039084)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.26 , pp. 8225-8235
    • Damm, K.L.1    Carlson, H.A.2
  • 43
    • 57349106476 scopus 로고    scopus 로고
    • Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking
    • Hritz, J.; de Ruiter, A.; Oostenbrink, C. Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking J. Med. Chem. 2008, 51, 7469-7477
    • (2008) J. Med. Chem. , vol.51 , pp. 7469-7477
    • Hritz, J.1    De Ruiter, A.2    Oostenbrink, C.3
  • 44
    • 0037157153 scopus 로고    scopus 로고
    • Computational drug design accommodating receptor flexibility: The relaxed complex scheme
    • DOI 10.1021/ja0260162
    • Lin, J.-H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme J. Am. Chem. Soc. 2002, 124, 5632-5633 (Pubitemid 34533490)
    • (2002) Journal of the American Chemical Society , vol.124 , Issue.20 , pp. 5632-5633
    • Lin, J.-H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 45
    • 65249157200 scopus 로고    scopus 로고
    • In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking
    • Bolstad, E. S. D.; Anderson, A. C. In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking Proteins: Struct., Funct., Bioinf. 2009, 75, 62-74
    • (2009) Proteins: Struct., Funct., Bioinf. , vol.75 , pp. 62-74
    • Bolstad, E.S.D.1    Anderson, A.C.2
  • 46
    • 57349156167 scopus 로고    scopus 로고
    • In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
    • DOI 10.1002/prot.22081
    • Bolstad, E. S. D.; Anderson, A. C. In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking Proteins: Struct., Funct., Bioinf. 2008, 73, 566-580 (Pubitemid 352788641)
    • (2008) Proteins: Structure, Function and Genetics , vol.73 , Issue.3 , pp. 566-580
    • Bolstad, E.S.D.1    Anderson, A.C.2
  • 47
    • 73349111930 scopus 로고    scopus 로고
    • Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization
    • Paulsen, J. L.; Anderson, A. C. Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization J. Chem. Inf. Model. 2009, 49, 2813-2819
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 2813-2819
    • Paulsen, J.L.1    Anderson, A.C.2
  • 48
    • 77951131275 scopus 로고    scopus 로고
    • Dynamic Ligand-Induced-Fit Simulation via Enhanced Conformational Samplings and Ensemble Dockings: A Survivin Example
    • Park, I.-H.; Li, C. Dynamic Ligand-Induced-Fit Simulation via Enhanced Conformational Samplings and Ensemble Dockings: A Survivin Example J. Phys. Chem. B 2010, 114, 5144-5153
    • (2010) J. Phys. Chem. B , vol.114 , pp. 5144-5153
    • Park, I.-H.1    Li, C.2
  • 49
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    • DOI 10.1021/jm8001197
    • Cheng, L. S.; Amaro, R. E.; Xu, D.; Li, W. W.; Arzberger, P. W.; McCammon, J. A. Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase J. Med. Chem. 2008, 51, 3878-3894 (Pubitemid 351956517)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.13 , pp. 3878-3894
    • Cheng, L.S.1    Amaro, R.E.2    Xu, D.3    Li, W.W.4    Arzberger, P.W.5    McCammon, J.A.6
  • 51
    • 1542741046 scopus 로고    scopus 로고
    • Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring
    • Yoon, S.; Welsh, W. J. Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring J. Chem. Inf. Comput. Sci. 2004, 44, 88-96
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 88-96
    • Yoon, S.1    Welsh, W.J.2
  • 52
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • DOI 10.1021/ja042260c
    • Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes J. Am. Chem. Soc. 2005, 127, 9632-9640 (Pubitemid 40934775)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.26 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 55
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J. Mol. Biol. 1995, 245, 43-53
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 56
    • 66249144110 scopus 로고    scopus 로고
    • Better than Random? the Chemotype Enrichment Problem
    • Mackey, M. D.; Melville, J. L. Better than Random? The Chemotype Enrichment Problem J. Chem. Inf. Model. 2009, 49, 1154-1162
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1154-1162
    • MacKey, M.D.1    Melville, J.L.2
  • 58
    • 26444468103 scopus 로고    scopus 로고
    • General and targeted statistical potentials for protein-ligand interactions
    • DOI 10.1002/prot.20588
    • Mooij, W. T. M.; Verdonk, M. L. General and targeted statistical potentials for protein-ligand interactions Proteins: Struct., Funct., Bioinf. 2005, 61, 272-287 (Pubitemid 41429135)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.2 , pp. 272-287
    • Mooij, W.T.M.1    Verdonk, M.L.2
  • 59
    • 0032153192 scopus 로고    scopus 로고
    • Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
    • Murray, C. W.; Auton, T. R.; Eldridge, M. D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model J. Comput.-Aided Mol. Des. 1998, 12, 503-519 (Pubitemid 128512820)
    • (1998) Journal of Computer-Aided Molecular Design , vol.12 , Issue.5 , pp. 503-519
    • Murray, C.W.1    Auton, T.R.2    Eldridge, M.D.3
  • 60
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes J. Comput.-Aided Mol. Des. 1997, 11, 425-445 (Pubitemid 127505895)
    • (1997) Journal of Computer-Aided Molecular Design , vol.11 , Issue.5 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 61
    • 62449330667 scopus 로고    scopus 로고
    • Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS
    • Korb, O.; Stützle, T.; Exner, T. E. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS J. Chem. Inf. Model. 2009, 49, 84-96
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 84-96
    • Korb, O.1    Stützle, T.2    Exner, T.E.3
  • 64
    • 0000490166 scopus 로고
    • From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders
    • Sadowski, J.; Gasteiger, J. From atoms and bonds to three-dimensional atomic coordinates: automatic model builders Chem. Rev. 1993, 93, 2567-2581
    • (1993) Chem. Rev. , vol.93 , pp. 2567-2581
    • Sadowski, J.1    Gasteiger, J.2
  • 65
    • 17144385534 scopus 로고    scopus 로고
    • Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
    • DOI 10.1021/jm049092j
    • Triballeau, N.; Acher, F.; Brabet, I.; Pin, J.-P.; Bertrand, H.-O. Virtual Screening Workflow Development Guided by the "Receiver Operating Characteristic" Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4 J. Med. Chem. 2005, 48, 2534-2547 (Pubitemid 40520517)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2534-2547
    • Triballeau, N.1    Acher, F.2    Brabet, I.3    Pin, J.-P.4    Bertrand, H.-O.5
  • 66
    • 41349122416 scopus 로고    scopus 로고
    • Optimization of CAMD techniques 3. Virtual screening enrichment studies: A help or hindrance in tool selection?
    • Good, A.; Oprea, T. Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J. Comput.-Aided Mol. Des. 2008, 22, 169-178
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 169-178
    • Good, A.1    Oprea, T.2
  • 67
    • 33646855259 scopus 로고    scopus 로고
    • version 7.5.2; Accelrys: San Diego, CA
    • Pipeline Pilot, version 7.5.2; Accelrys: San Diego, CA, 2009.
    • (2009) Pipeline Pilot
  • 68
    • 77952772341 scopus 로고    scopus 로고
    • Extended-Connectivity Fingerprints
    • Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 742-754
    • Rogers, D.1    Hahn, M.2
  • 69
    • 82355182425 scopus 로고    scopus 로고
    • The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance
    • Korb, O.; McCabe, P.; Cole, J. The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance. J. Chem. Inf. Model. 2915-2919.
    • J. Chem. Inf. Model. , pp. 2915-2919
    • Korb, O.1    McCabe, P.2    Cole, J.3
  • 70
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • DOI 10.1021/jm0300330
    • McGovern, S. L.; Shoichet, B. K. Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes J. Med. Chem. 2003, 46, 2895-2907 (Pubitemid 36775915)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.14 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.