-
1
-
-
84866739808
-
Drug Discovery in Pharmaceutical Industry: Productivity Challenges and Trends
-
Khanna, I. Drug Discovery in Pharmaceutical Industry: Productivity Challenges and Trends Drug Discovery Today 2012, 17, 1088-1102
-
(2012)
Drug Discovery Today
, vol.17
, pp. 1088-1102
-
-
Khanna, I.1
-
2
-
-
34447275949
-
Ligand Docking and Structure-based Virtual Screening in Drug Discovery
-
Cavasotto, C. N.; Orry, A. J. W. Ligand Docking and Structure-based Virtual Screening in Drug Discovery Curr. Top. Med. Chem. 2007, 7, 1006-1014
-
(2007)
Curr. Top. Med. Chem.
, vol.7
, pp. 1006-1014
-
-
Cavasotto, C.N.1
Orry, A.J.W.2
-
3
-
-
84875150414
-
The Holistic Integration of Virtual Screening in Drug Discovery
-
Tanrikulu, Y.; Krüger, B.; Proschak, E. The Holistic Integration of Virtual Screening in Drug Discovery Drug Discovery Today 2013, 18, 358-364
-
(2013)
Drug Discovery Today
, vol.18
, pp. 358-364
-
-
Tanrikulu, Y.1
Krüger, B.2
Proschak, E.3
-
4
-
-
84874298502
-
How Far Can Virtual Screening Take us in Drug Discovery?
-
Kar, S.; Roy, K. How Far Can Virtual Screening Take us in Drug Discovery? Expert Opin. Drug Discovery 2013, 8, 245-261
-
(2013)
Expert Opin. Drug Discovery
, vol.8
, pp. 245-261
-
-
Kar, S.1
Roy, K.2
-
5
-
-
84862027743
-
Recognizing Pitfalls in Virtual Screening: A Critical Review
-
Scior, T.; Bender, A.; Tresadern, G.; Medina-Franco, J. L.; Martínez-Mayorga, K.; Langer, T.; Cuanalo-Contreras, K.; Agrafiotis, D. K. Recognizing Pitfalls in Virtual Screening: A Critical Review J. Chem. Inf. Model. 2012, 52, 867-881
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 867-881
-
-
Scior, T.1
Bender, A.2
Tresadern, G.3
Medina-Franco, J.L.4
Martínez- Mayorga, K.5
Langer, T.6
Cuanalo-Contreras, K.7
Agrafiotis, D.K.8
-
6
-
-
84879242302
-
Combination of Ligand- and Structure-Based Methods in Virtual Screening
-
Drwal, M. N.; Griffith, R. Combination of Ligand- and Structure-Based Methods in Virtual Screening Drug Discovery Today: Technologies 2013, 10, e395-e401
-
(2013)
Drug Discovery Today: Technologies
, vol.10
-
-
Drwal, M.N.1
Griffith, R.2
-
7
-
-
33749260698
-
A Critical Assessment of Docking Programs and Scoring Functions
-
Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions J. Med. Chem. 2006, 49, 5912-5931
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
Lalonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
8
-
-
11644261806
-
Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function J. Comput. Chem. 1998, 19, 1639-1662
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
9
-
-
76149120388
-
AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization and Multithreading
-
Trott, O.; Olson, A. J. AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization and Multithreading J. Comput. Chem. 2010, 31, 455-461
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
10
-
-
69249127027
-
Blind Docking of Pharmaceutically Relevant Compounds Using RosettaLigand
-
Davis, I. W.; Raha, K.; Head, M. S.; Baker, D. Blind Docking of Pharmaceutically Relevant Compounds Using RosettaLigand Protein Sci. 2009, 18, 1998-2002
-
(2009)
Protein Sci.
, vol.18
, pp. 1998-2002
-
-
Davis, I.W.1
Raha, K.2
Head, M.S.3
Baker, D.4
-
11
-
-
77954063262
-
Rescoring Ligand Docking Poses
-
Zhong, S.; Zhang, Y.; Xiu, Z. Rescoring Ligand Docking Poses Curr. Opin. Drug Discovery Dev. 2010, 13, 326-34
-
(2010)
Curr. Opin. Drug Discovery Dev.
, vol.13
, pp. 326-334
-
-
Zhong, S.1
Zhang, Y.2
Xiu, Z.3
-
12
-
-
34249278087
-
Ranking Poses in Structure-Based Lead Discovery and Optimization: Current Trends in Scoring Function Development
-
Rajamani, R.; Good, A. C. Ranking Poses in Structure-Based Lead Discovery and Optimization: Current Trends in Scoring Function Development Curr. Opin. Drug Discovery Dev. 2007, 10, 308-15
-
(2007)
Curr. Opin. Drug Discovery Dev.
, vol.10
, pp. 308-315
-
-
Rajamani, R.1
Good, A.C.2
-
13
-
-
42449152858
-
The Use of Protein-Ligand Interaction Fingerprints in Docking
-
Brewerton, S. C. The Use of Protein-Ligand Interaction Fingerprints in Docking Curr. Opin. Drug Discovery Dev. 2008, 11, 356-64
-
(2008)
Curr. Opin. Drug Discovery Dev.
, vol.11
, pp. 356-364
-
-
Brewerton, S.C.1
-
14
-
-
72449144245
-
Drug Efficiency Indices for Improvement of Molecular Docking Scoring Functions
-
García-Sosa, A. T.; Hetényi, C.; Maran, U. Drug Efficiency Indices for Improvement of Molecular Docking Scoring Functions J. Comput. Chem. 2010, 31, 174-184
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 174-184
-
-
García-Sosa, A.T.1
Hetényi, C.2
Maran, U.3
-
15
-
-
38549178026
-
A Statistical Rescoring Scheme for Protein-Ligand Docking: Consideration of Entropic Effect
-
Lee, J.; Seok, C. A Statistical Rescoring Scheme for Protein-Ligand Docking: Consideration of Entropic Effect Proteins 2008, 70, 1074-1083
-
(2008)
Proteins
, vol.70
, pp. 1074-1083
-
-
Lee, J.1
Seok, C.2
-
16
-
-
80051998385
-
Normalizing Molecular Docking Rankings Using Virtually Generated Decoys
-
Wallach, I.; Jaitly, N.; Nguyen, K.; Schapira, M.; Lilien, R. Normalizing Molecular Docking Rankings Using Virtually Generated Decoys J. Chem. Inf. Model. 2011, 51, 1817-1830
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1817-1830
-
-
Wallach, I.1
Jaitly, N.2
Nguyen, K.3
Schapira, M.4
Lilien, R.5
-
17
-
-
33748667774
-
Consensus Scoring for Protein-Ligand Interactions
-
Feher, M. Consensus Scoring for Protein-Ligand Interactions Drug Discovery Today 2006, 11, 421-428
-
(2006)
Drug Discovery Today
, vol.11
, pp. 421-428
-
-
Feher, M.1
-
18
-
-
0036136868
-
Consensus Scoring for Ligand/Protein Interactions
-
Clark, R. D.; Strizhev, A.; Leonard, J. M.; Blake, J. F.; Matthew, J. B. Consensus Scoring for Ligand/Protein Interactions J. Mol. Graph. Model. 2002, 20, 281-295
-
(2002)
J. Mol. Graph. Model.
, vol.20
, pp. 281-295
-
-
Clark, R.D.1
Strizhev, A.2
Leonard, J.M.3
Blake, J.F.4
Matthew, J.B.5
-
19
-
-
23844555629
-
Consensus Scoring Criteria for Improving Enrichment in Virtual Screening
-
Yang, J. M.; Chen, Y. F.; Shen, T. W.; Kristal, B. S.; Hsu, D. F. Consensus Scoring Criteria for Improving Enrichment in Virtual Screening J. Chem. Inf. Model. 2005, 45, 1134-1146
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 1134-1146
-
-
Yang, J.M.1
Chen, Y.F.2
Shen, T.W.3
Kristal, B.S.4
Hsu, D.F.5
-
20
-
-
0346996357
-
Improving Structure-Based Virtual Screening by Multivariate Analysis of Scoring Data
-
Jacobsson, M.; Lidén, P.; Stjernschantz, E.; Boström, H.; Norinder, U. Improving Structure-Based Virtual Screening by Multivariate Analysis of Scoring Data J. Med. Chem. 2003, 46, 5781-5789
-
(2003)
J. Med. Chem.
, vol.46
, pp. 5781-5789
-
-
Jacobsson, M.1
Lidén, P.2
Stjernschantz, E.3
Boström, H.4
Norinder, U.5
-
21
-
-
33750991346
-
Benchmarking Sets for Molecular Docking
-
Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking Sets for Molecular Docking J. Med. Chem. 2006, 49, 6789-6801
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
22
-
-
70349932423
-
Autodock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexiblity
-
Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. Autodock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexiblity J. Comput. Chem. 2009, 16, 2785-91
-
(2009)
J. Comput. Chem.
, vol.16
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.J.7
-
23
-
-
33750056673
-
ROSETTALIGAND: Protein-Small Molecule Docking with Full Side-Chain Flexibility
-
Meiler, J.; Baker, D. ROSETTALIGAND: Protein-Small Molecule Docking with Full Side-Chain Flexibility Proteins 2006, 65, 538-548
-
(2006)
Proteins
, vol.65
, pp. 538-548
-
-
Meiler, J.1
Baker, D.2
-
24
-
-
84855945133
-
Rosetta Ligand Docking with Flexible XML Protocols
-
In; Baron, R. Springer: New York, Vol.
-
Lemmon, G.; Meiler, J. Rosetta Ligand Docking with Flexible XML Protocols. In Computational Drug Discovery and Design; Baron, R., Ed.; Springer: New York, 2012; Vol. 819, pp 143-155.
-
(2012)
Computational Drug Discovery and Design
, vol.819
, pp. 143-155
-
-
Lemmon, G.1
Meiler, J.2
-
25
-
-
77951986384
-
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
-
26
-
-
79959615159
-
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
-
Fleishman, S. J.; Leaver-Fay, A.; Corn, J. E.; Strauch, E. M.; Khare, S. D.; Koga, N.; Ashworth, J.; Murphy, P.; Richter, F.; Lemmon, G.; Meiler, J.; Baker, D. RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite PLoS One 2011, 6, e20161
-
(2011)
PLoS One
, vol.6
, pp. 20161
-
-
Fleishman, S.J.1
Leaver-Fay, A.2
Corn, J.E.3
Strauch, E.M.4
Khare, S.D.5
Koga, N.6
Ashworth, J.7
Murphy, P.8
Richter, F.9
Lemmon, G.10
Meiler, J.11
Baker, D.12
-
27
-
-
58149094776
-
ROSETTALIGAND Docking with Full Ligand and Receptor Flexibility
-
Davis, I. W.; Baker, D. ROSETTALIGAND Docking with Full Ligand and Receptor Flexibility J. Mol. Biol. 2009, 385, 381-392
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 381-392
-
-
Davis, I.W.1
Baker, D.2
-
28
-
-
80053512597
-
Open Babel: An Open Chemical Toolbox
-
O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An Open Chemical Toolbox J. Cheminform. 2011, 3, 33
-
(2011)
J. Cheminform.
, vol.3
, pp. 33
-
-
O'Boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
29
-
-
0043126911
-
Logistic Regression and Artificial Neural Network Classification Models: A Methodology Review
-
Dreiseitl, S.; Ohno-Machado, L. Logistic Regression and Artificial Neural Network Classification Models: a Methodology Review J. Biomed. Inform. 2002, 35, 352-359
-
(2002)
J. Biomed. Inform.
, vol.35
, pp. 352-359
-
-
Dreiseitl, S.1
Ohno-Machado, L.2
-
30
-
-
77949523247
-
PyBrain
-
Schaul, T.; Bayer, J.; Wierstra, D.; Sun, Y.; Felder, M.; Sehnke, F.; Rückstieß, T.; Schmidhuber, J. PyBrain J. Mach. Learn. Res. 2010, 11, 743-746
-
(2010)
J. Mach. Learn. Res.
, vol.11
, pp. 743-746
-
-
Schaul, T.1
Bayer, J.2
Wierstra, D.3
Sun, Y.4
Felder, M.5
Sehnke, F.6
Rückstieß, T.7
Schmidhuber, J.8
-
31
-
-
41349093326
-
What Do We Know and When Do We Know it?
-
Nicholls, A. What Do We Know and When Do We Know it? J. Comput.-Aided Mol. Des. 2008, 22, 239-255
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 239-255
-
-
Nicholls, A.1
-
32
-
-
82355186299
-
NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function
-
Durrant, J. D.; McCammon, J. A. NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function J. Chem. Inf. Model. 2011, 51, 2897-2903
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2897-2903
-
-
Durrant, J.D.1
McCammon, J.A.2
-
33
-
-
77957820654
-
Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina
-
Chang, M. W.; Ayeni, C.; Breuer, S.; Torbett, B. E. Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina PLoS One 2010, 5, e11955
-
(2010)
PLoS One
, vol.5
, pp. 11955
-
-
Chang, M.W.1
Ayeni, C.2
Breuer, S.3
Torbett, B.E.4
-
34
-
-
84871122167
-
Using RosettaLigand for Small Molecule Docking into Comparative Models
-
Kaufmann, K. W.; Meiler, J. Using RosettaLigand for Small Molecule Docking into Comparative Models PLoS One 2012, 7, e50769
-
(2012)
PLoS One
, vol.7
, pp. 50769
-
-
Kaufmann, K.W.1
Meiler, J.2
-
35
-
-
67650097331
-
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
-
Cross, J. B.; Thompson, D. C.; Rai, B. K.; Baber, J. C.; Fan, K. Y.; Hu, Y.; Humblet, C. Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy J. Chem. Inf. Model. 2009, 49, 1455-1474
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.6
Humblet, C.7
-
36
-
-
84865265287
-
Docking and Scoring with ICM: The Benchmarking Results and Strategies for Improvement
-
Neves, M. A.; Totrov, M.; Abagyan, R. Docking and Scoring with ICM: The Benchmarking Results and Strategies for Improvement J. Comput. Aided Mol. Des. 2012, 26, 675-686
-
(2012)
J. Comput. Aided Mol. Des.
, vol.26
, pp. 675-686
-
-
Neves, M.A.1
Totrov, M.2
Abagyan, R.3
-
37
-
-
84880552522
-
Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening
-
Durrant, J. D.; Friedman, A. J.; Rogers, K. E.; McCammon, J. A. Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening J. Chem. Inf. Model. 2013, 53, 1726-1735
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1726-1735
-
-
Durrant, J.D.1
Friedman, A.J.2
Rogers, K.E.3
McCammon, J.A.4
-
38
-
-
77958585233
-
NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes
-
Durrant, J. D.; McCammon, J. A. NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes J. Chem. Inf. Model. 2010, 50, 1865-1871
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1865-1871
-
-
Durrant, J.D.1
McCammon, J.A.2
-
39
-
-
84874445951
-
Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
-
Houston, D. R.; Walkinshaw, M. D. Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context J. Chem. Inf. Model. 2013, 53, 384-390
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 384-390
-
-
Houston, D.R.1
Walkinshaw, M.D.2
-
40
-
-
79955388686
-
Improving VEGFR-2 Docking-Based Screening by Pharmacophore Postfiltering and Similarity Search Postprocessing
-
Planesas, J. M.; Claramunt, R. M.; Teixidó, J.; Borrell, J. I.; Pérez-Nueno, V. I. Improving VEGFR-2 Docking-Based Screening by Pharmacophore Postfiltering and Similarity Search Postprocessing J. Chem. Inf. Model. 2011, 51, 777-787
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 777-787
-
-
Planesas, J.M.1
Claramunt, R.M.2
Teixidó, J.3
Borrell, J.I.4
Pérez-Nueno, V.I.5
-
41
-
-
34247262566
-
Supervised Consensus Scoring for Docking and Virtual Screening
-
Teramoto, R.; Fukunishi, H. Supervised Consensus Scoring for Docking and Virtual Screening J. Chem. Inf. Model. 2007, 47, 526-534
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 526-534
-
-
Teramoto, R.1
Fukunishi, H.2
-
42
-
-
33750063262
-
Combinatorial Fusion Analysis: Methods and Practice of Combining Multiple Scoring Systems
-
In; IGI Global
-
Hsu, D. F.; Chung, Y.-S.; Kristal, B. S., Combinatorial Fusion Analysis: Methods and Practice of Combining Multiple Scoring Systems. In Data Warehousing and Mining: Concepts, Methodologies, Tools, and Applications; IGI Global, 2008; pp 1157-1181.
-
(2008)
Data Warehousing and Mining: Concepts, Methodologies, Tools, and Applications
, pp. 1157-1181
-
-
Hsu, D.F.1
Chung, Y.-S.2
Kristal, B.S.3
-
43
-
-
78249232295
-
Rank-Score Characteristics (RSC) Function and Cognitive Diversity
-
In; Yao, Y. Sun, R. Poggio, T. Liu, J. Zhong, N. Huang, J. Springer: Berlin and Heidelberg, Vol.
-
Hsu, D. F.; Kristal, B.; Schweikert, C., Rank-Score Characteristics (RSC) Function and Cognitive Diversity. In Brain Informatics; Yao, Y.; Sun, R.; Poggio, T.; Liu, J.; Zhong, N.; Huang, J., Eds.; Springer: Berlin and Heidelberg, 2010; Vol. 6334, pp 42-54.
-
(2010)
Brain Informatics
, vol.6334
, pp. 42-54
-
-
Hsu, D.F.1
Kristal, B.2
Schweikert, C.3
|