-
1
-
-
0038792292
-
Discovery of a Potent and Selective Protein Kinase CK2 Inhibitor by High-Throughput Docking
-
Vangrevelinghe, E.; Zimmermann, K.; Schoepfer, J.; Portmann, R.; Fabbro, D.; Furet, P. Discovery of a Potent and Selective Protein Kinase CK2 Inhibitor by High-Throughput Docking. J. Med. Chem. 2003, 46, 2656-2662.
-
(2003)
J. Med. Chem
, vol.46
, pp. 2656-2662
-
-
Vangrevelinghe, E.1
Zimmermann, K.2
Schoepfer, J.3
Portmann, R.4
Fabbro, D.5
Furet, P.6
-
2
-
-
1642357706
-
The Many Roles of Computation in Drug Discovery
-
Jorgensen, W. L. The Many Roles of Computation in Drug Discovery. Science 2004, 303, 1813-1818.
-
(2004)
Science
, vol.303
, pp. 1813-1818
-
-
Jorgensen, W.L.1
-
3
-
-
33644854957
-
Identification of Novel Parasitic Cysteine Protease Inhibitors by Use of Virtual Screening. 2. The Available Chemical Directory
-
Desai, P. V.; Patny, A.; Gut, J.; Rosenthal, P. J.; Tekwani, B.; Srivastava, A.; Avery, M. Identification of Novel Parasitic Cysteine Protease Inhibitors by Use of Virtual Screening. 2. The Available Chemical Directory. J. Med. Chem. 2006, 49, 1576-1584.
-
(2006)
J. Med. Chem
, vol.49
, pp. 1576-1584
-
-
Desai, P.V.1
Patny, A.2
Gut, J.3
Rosenthal, P.J.4
Tekwani, B.5
Srivastava, A.6
Avery, M.7
-
4
-
-
33646442795
-
In Silico Discovery of Beta-Secretase Inhibitors
-
Huang, D. Z.; Luthi, U.; Kolb, P.; Cecchini, M.; Barberis, A.; Caflisch, A. In Silico Discovery of Beta-Secretase Inhibitors. J. Am. Chem. Soc. 2006, 128, 5436-5443.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 5436-5443
-
-
Huang, D.Z.1
Luthi, U.2
Kolb, P.3
Cecchini, M.4
Barberis, A.5
Caflisch, A.6
-
5
-
-
33745405015
-
High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing
-
Brown, S. P.; Muchmore, S. W. High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing. J. Chem. Inf. Model. 2006, 46, 999-1005.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 999-1005
-
-
Brown, S.P.1
Muchmore, S.W.2
-
6
-
-
41649096077
-
Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model
-
Kolb, P.; Huang, D.; Dey, F.; Caflisch, A. Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model. J. Med. Chem. 2008, 51, 1179-1188.
-
(2008)
J. Med. Chem
, vol.51
, pp. 1179-1188
-
-
Kolb, P.1
Huang, D.2
Dey, F.3
Caflisch, A.4
-
7
-
-
50849118847
-
Structure-Based Tailoring of Compound Libraries for High-Throughput Screening: Discovery of Novel EphB4 Kinase Inhibitors
-
Kolb, P.; Kipouros, C. B.; Huang, D.; Caflisch, A. Structure-Based Tailoring of Compound Libraries for High-Throughput Screening: Discovery of Novel EphB4 Kinase Inhibitors. Proteins 2008, 73, 11-18.
-
(2008)
Proteins
, vol.73
, pp. 11-18
-
-
Kolb, P.1
Kipouros, C.B.2
Huang, D.3
Caflisch, A.4
-
8
-
-
12144289984
-
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J. Med. Chem. 2004, 47, 1739-1749.
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J. Med. Chem. 2004, 47, 1739-1749.
-
-
-
-
9
-
-
1642310340
-
-
Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening. J. Med. Chem. 2004, 47, 1750-1759.
-
Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening. J. Med. Chem. 2004, 47, 1750-1759.
-
-
-
-
11
-
-
40749120187
-
An Implementation for High-Throughput Virtual Screening Using AutoDock
-
Zhang, S. X.; Kumar, K.; Jiang, X. H.; Wallqvist, A.; Reifman, J. DOVIS: An Implementation for High-Throughput Virtual Screening Using AutoDock. Bmc Bioinformatics 2008, 9.
-
(2008)
Bmc Bioinformatics
, pp. 9
-
-
Zhang, S.X.1
Kumar, K.2
Jiang, X.H.3
Wallqvist, A.4
Reifman5
DOVIS, J.6
-
12
-
-
0020491251
-
A Geometric Approach To Macromolecule-Ligand Interactions
-
Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A Geometric Approach To Macromolecule-Ligand Interactions. J. Mol. Biol. 1982, 161, 269-288.
-
(1982)
J. Mol. Biol
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
13
-
-
33845873363
-
Development and Validation of a Modular, Extensible Docking Program: DOCK 5
-
Moustakas, D. T.; Lang, P. T.; Pegg, S.; Pettersen, E.; Kuntz, I. D.; Brooijmans, N.; Rizzo, R. C. Development and Validation of a Modular, Extensible Docking Program: DOCK 5. J. Comput.-Aided Mol. Des. 2006, 20, 601-619.
-
(2006)
J. Comput.-Aided Mol. Des
, vol.20
, pp. 601-619
-
-
Moustakas, D.T.1
Lang, P.T.2
Pegg, S.3
Pettersen, E.4
Kuntz, I.D.5
Brooijmans, N.6
Rizzo, R.C.7
-
14
-
-
79952512133
-
-
RedPaper 2008, REDP-4410-00
-
Peters, A.; Lundberg, M. E.; Lang, P. T.; Sosa, C. P. High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System. RedPaper 2008, REDP-4410-00.
-
High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System
-
-
Peters, A.1
Lundberg, M.E.2
Lang, P.T.3
Sosa, C.P.4
-
15
-
-
61949324945
-
-
Mullen-Schultz, G. L.; Sosa, C. P. IBM System Blue Gene Solution. Application Development. 2007, SG24-7179.
-
Mullen-Schultz, G. L.; Sosa, C. P. IBM System Blue Gene Solution. Application Development. 2007, SG24-7179.
-
-
-
-
16
-
-
33845511093
-
Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking
-
Kolb, P.; Caflisch, A. Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking. J. Med. Chem. 2006, 49, 7384-7392.
-
(2006)
J. Med. Chem
, vol.49
, pp. 7384-7392
-
-
Kolb, P.1
Caflisch, A.2
-
18
-
-
84986512474
-
Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
19
-
-
84988129057
-
Optimization of Parameters for Semiempirical Methods I. Method
-
Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods I. Method. J. Comput. Chem. 1989, 10, 209-220.
-
(1989)
J. Comput. Chem
, vol.10
, pp. 209-220
-
-
Stewart, J.J.P.1
-
20
-
-
7444257387
-
Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation
-
Huang, D.; Caflisch, A. Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation. J. Med. Chem. 2004, 47, 5791-5797.
-
(2004)
J. Med. Chem
, vol.47
, pp. 5791-5797
-
-
Huang, D.1
Caflisch, A.2
-
21
-
-
47749108669
-
-
Zhou, T.; Huang, D.; Caflisch, A. Is Quantum Mechanics Necessary for Predicting Binding Free Energy. J. Med. Chem. 2008, 51, 4280-4288.
-
Zhou, T.; Huang, D.; Caflisch, A. Is Quantum Mechanics Necessary for Predicting Binding Free Energy. J. Med. Chem. 2008, 51, 4280-4288.
-
-
-
-
22
-
-
0033576680
-
Consensus scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-dimensional Structures into Proteins
-
Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-dimensional Structures into Proteins. J. Med. Chem. 1999, 42, 5100-5109.
-
(1999)
J. Med. Chem
, vol.42
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
23
-
-
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. Graphics Modell. 2002, 20, 281-295.
-
(2002)
J. Mol. Graphics Modell
, vol.20
, pp. 281-295
-
-
Clark, R.D.1
Strizhev, A.2
Leonard, J.M.3
Blake, J.F.4
Matthew, J.B.5
-
24
-
-
0035312864
-
Statistical Potentials and Scoring Functions Applied to Protein-ligand Binding
-
Gohlke, H.; Klebe, G. Statistical Potentials and Scoring Functions Applied to Protein-ligand Binding. Curr. Opin. Struct. Biol. 2001, 11, 231-235.
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, pp. 231-235
-
-
Gohlke, H.1
Klebe, G.2
-
25
-
-
13844312649
-
-
Irwin, J. J.; Shoichet, B. K. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J. Chem. Inf. Model. 2005, 45, 177-182.
-
Irwin, J. J.; Shoichet, B. K. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J. Chem. Inf. Model. 2005, 45, 177-182.
-
-
-
-
26
-
-
84986505827
-
Validation of the General-Purpose Quanta(R)3.2/Charmm(R) Force-Field
-
Momany, F. A.; Rone, R. Validation of the General-Purpose Quanta(R)3.2/Charmm(R) Force-Field. J. Comput. Chem. 1992, 13, 888-900.
-
(1992)
J. Comput. Chem
, vol.13
, pp. 888-900
-
-
Momany, F.A.1
Rone, R.2
-
27
-
-
61949398579
-
-
0.4.6; Michael Bayer: New York, NY
-
SQLAlchemy, 0.4.6; Michael Bayer: New York, NY, 2008.
-
(2008)
SQLAlchemy
-
-
-
28
-
-
61949393408
-
-
G. Elixir, accessed 31, Oct, 2008
-
LaCour, J.; Haus, D.; Menten, d. G. Elixir. http://elixir.ematia.de/trac/ (accessed 31, Oct, 2008).
-
Menten, d
-
-
LaCour, J.1
Haus, D.2
-
29
-
-
61949423275
-
-
MySQL::MySQL 5.1 Reference Manual:: 17.2.3 HASH Partitioning. http://dev.mysql.com/doc/refman/5.1/en/partitioning-hash.html (accessed 31, Oct, 2008).
-
MySQL::MySQL 5.1 Reference Manual:: 17.2.3 HASH Partitioning. http://dev.mysql.com/doc/refman/5.1/en/partitioning-hash.html (accessed 31, Oct, 2008).
-
-
-
-
30
-
-
61949243841
-
-
MySQL::MySQL 5.0 Reference Manual::13.1 The MyISAM Storage Engine. http://dev.mysql.com/doc/rnysql/en/myisam-storage-engine.html (accessed 31, Oct, 2008).
-
MySQL::MySQL 5.0 Reference Manual::13.1 The MyISAM Storage Engine. http://dev.mysql.com/doc/rnysql/en/myisam-storage-engine.html (accessed 31, Oct, 2008).
-
-
-
-
31
-
-
61949353786
-
-
InnoDB Website, accessed 31, Oct, 2008
-
InnoDB Website. http://www.innodb.com/(accessed 31, Oct, 2008).
-
-
-
-
32
-
-
61949173172
-
-
Gailly, J.; Adler, M. zlib Home Site. http://www.zlib.net/(accessed 31, Oct, 2008).
-
Gailly, J.; Adler, M. zlib Home Site. http://www.zlib.net/(accessed 31, Oct, 2008).
-
-
-
-
33
-
-
61949432743
-
-
MySQL::MySQL 5.1 Reference Manual::10.5 Data Type Storage Requirements. http://dev.mysql.com/doc/refman/5.1/en/storage-requirements.html (accessed 31, Oct, 2008).
-
MySQL::MySQL 5.1 Reference Manual::10.5 Data Type Storage Requirements. http://dev.mysql.com/doc/refman/5.1/en/storage-requirements.html (accessed 31, Oct, 2008).
-
-
-
-
34
-
-
61949248955
-
-
ADT/AutoDockTools-AutoDock, accessed 31, Oct, 2008
-
ADT/AutoDockTools-AutoDock. http://autodock.scripps.edu/resources/adt/ index-html (accessed 31, Oct, 2008).
-
-
-
|