-
1
-
-
0027385177
-
Matching chemistry and shape in molecular docking
-
Shoichet, B. K.; Kuntz, I. D. Matching Chemistry and Shape in Molecular Docking. Protein Eng. 1993, 6, 723-732.
-
(1993)
Protein Eng.
, vol.6
, pp. 723-732
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
2
-
-
0001016942
-
Structure-based molecular design
-
Kuntz, I. D.; Meng, E. C.; Shoichet, B. K. Structure-Based Molecular Design. Acc. Chem. Res. 1994, 27, 117-123.
-
(1994)
Acc. Chem. Res.
, vol.27
, pp. 117-123
-
-
Kuntz, I.D.1
Meng, E.C.2
Shoichet, B.K.3
-
3
-
-
0030111106
-
Molecular docking towards drug discovery
-
Gschwend, D. A.; Good, A. C.; Kuntz, I. D. Molecular docking towards drug discovery. J. Mol. Recognit. 1996, 9, 175-186.
-
(1996)
J. Mol. Recognit.
, vol.9
, pp. 175-186
-
-
Gschwend, D.A.1
Good, A.C.2
Kuntz, I.D.3
-
4
-
-
0029283717
-
Flexible ligand docking using a genetic algorithm
-
Oshiro, C. M.; Kuntz, I. D.; Dixon, J. S. Flexible Ligand Docking Using a Genetic Algorithm. J. Comput.-Aided Mol. Des. 1995, 9, 113-130.
-
(1995)
J. Comput.-aided Mol. Des.
, vol.9
, pp. 113-130
-
-
Oshiro, C.M.1
Kuntz, I.D.2
Dixon, J.S.3
-
5
-
-
0029705324
-
Automated docking of flexible ligands: Applications of AutoDock
-
Goodsell, D. S.; Morris, G. M.; Olson, A. J. Automated docking of flexible ligands: Applications of AutoDock. J. Mol. Recognit. 1996, 9, 1-5.
-
(1996)
J. Mol. Recognit.
, vol.9
, pp. 1-5
-
-
Goodsell, D.S.1
Morris, G.M.2
Olson, A.J.3
-
6
-
-
0036137713
-
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
-
Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002, 46, 34-40.
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
7
-
-
0035765452
-
Small molecule docking and scoring
-
Lipkowitz, K. B., Boyd, D. B., Eds.; John Wiley & Sons
-
Muegge, I.; Rarey, M. Small Molecule Docking and Scoring. In Reviews in Computational Chemistry, 17th ed.; Lipkowitz, K. B., Boyd, D. B., Eds.; John Wiley & Sons: 2001.
-
(2001)
Reviews in Computational Chemistry, 17th Ed.
-
-
Muegge, I.1
Rarey, M.2
-
8
-
-
8744243346
-
Molecular-dynamics and free-energy perturbation calculations - What role do they play in computer-assisted molecular design
-
Kollman, P. Molecular-Dynamics and Free-Energy Perturbation Calculations - What Role Do They Play in Computer-Assisted Molecular Design. FASEB J. 1995, 9, A1253-A1253.
-
(1995)
FASEB J.
, vol.9
-
-
Kollman, P.1
-
9
-
-
7044239742
-
Free-energy calculations - Applications to chemical and biochemical phenomena
-
Kollman, P. Free-Energy Calculations - Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417.
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
10
-
-
0036280661
-
Ligand binding affinities from MD simulations
-
Aqvist, J.; Luzhkov, V. B.; Brandsdal, B. O. Ligand binding affinities from MD simulations. Acc. Chem. Res. 2002, 35, 358-365.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 358-365
-
-
Aqvist, J.1
Luzhkov, V.B.2
Brandsdal, B.O.3
-
11
-
-
0028155689
-
New method for predicting binding-affinity in computer-aided drug design
-
Aqvist, J.; Medina, C.; Samuelsson, J. E. New Method for Predicting Binding-Affinity in Computer-Aided Drug Design. Protein Eng. 1994, 7, 385-391.
-
(1994)
Protein Eng.
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
12
-
-
0346052295
-
Calculation of the hydration free energies using an extended linear response method
-
Chen, X.; Tropsha, A. Calculation of the hydration free energies using an extended linear response method. J. Comput. Chem. 1999, 20, 749-759.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 749-759
-
-
Chen, X.1
Tropsha, A.2
-
13
-
-
0035950792
-
New linear interaction method for binding affinity calculations using a continuum solvent model
-
Zhou, R. H.; Friesner, R. A.; Ghosh, A.; Rizzo, R. C.; Jorgensen, W. L.; Levy, R. M. New linear interaction method for binding affinity calculations using a continuum solvent model. J. Phys. Chem. B 2001, 105, 10388-10397.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 10388-10397
-
-
Zhou, R.H.1
Friesner, R.A.2
Ghosh, A.3
Rizzo, R.C.4
Jorgensen, W.L.5
Levy, R.M.6
-
14
-
-
20444411998
-
Recent trends in quantitative structure-activity relationships
-
Abraham, D., Ed.; John Wiley & Sons: New York
-
Tropsha, A. Recent Trends in Quantitative Structure-Activity Relationships. In Burger's Medicinal Chemistry and Drug Discovery, 6th ed.; Abraham, D., Ed.; John Wiley & Sons: New York, 2003; pp 49-77.
-
(2003)
Burger's Medicinal Chemistry and Drug Discovery, 6th Ed.
, pp. 49-77
-
-
Tropsha, A.1
-
15
-
-
0000353230
-
The characterization of chemical structures using molecular properties
-
Livingstone, D. J. The characterization of chemical structures using molecular properties. J. Chem. Inf. Comput. Sci 2000, 40, 195-209.
-
(2000)
J. Chem. Inf. Comput. Sci
, vol.40
, pp. 195-209
-
-
Livingstone, D.J.1
-
16
-
-
0033968062
-
Chemoinformatics - Similarity and diversity in chemical libraries
-
Willett, P. Chemoinformatics - similarity and diversity in chemical libraries. Curr. Opin. Biotechnol. 2000, 11, 85-88.
-
(2000)
Curr. Opin. Biotechnol.
, vol.11
, pp. 85-88
-
-
Willett, P.1
-
17
-
-
0033980580
-
Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA)
-
Turner, D. B.; Willett, P. Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA). J. Comput.-Aided Mol. Des. 2000, 14, 1-21.
-
(2000)
J. Comput.-aided Mol. Des.
, vol.14
, pp. 1-21
-
-
Turner, D.B.1
Willett, P.2
-
18
-
-
0000886672
-
Electron density modeling of large systems using the transferable atom equivalent method
-
Breneman, C. M.; Thompson, T. R.; Rhem, M; Dung, M. Electron Density Modeling of Large Systems using the Transferable Atom Equivalent Method. Comput. Chem. 1995, 19, 161-169.
-
(1995)
Comput. Chem.
, vol.19
, pp. 161-169
-
-
Breneman, C.M.1
Thompson, T.R.2
Rhem, M.3
Dung, M.4
-
19
-
-
0035891173
-
Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure
-
Mazza, C. B.; Sukumar, N.; Breneman, C. M.; Cramer, S. M. Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure. Anal. Chem. 2001, 73, 5457-5461.
-
(2001)
Anal. Chem.
, vol.73
, pp. 5457-5461
-
-
Mazza, C.B.1
Sukumar, N.2
Breneman, C.M.3
Cramer, S.M.4
-
20
-
-
0036827078
-
Prediction of protein retention times in anion-exchange chromatography systems using support vector regression
-
Song, M.; Breneman, C. M.; Bi, J.; Sukumar, N.; Bennett. K. P.; Cramer, S.; Tugcu, N. Prediction of protein retention times in anion-exchange chromatography systems using support vector regression. J. Chem. Inf. Comput. Sci. 2002, 42, 1347-1357.
-
(2002)
J. Chem. Inf. Comput. Sci.
, vol.42
, pp. 1347-1357
-
-
Song, M.1
Breneman, C.M.2
Bi, J.3
Sukumar, N.4
Bennett, K.P.5
Cramer, S.6
Tugcu, N.7
-
21
-
-
2542530042
-
The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 2004, 47, 2977-2980.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
22
-
-
28544445099
-
-
Tripos, Inc., St. Louis, MO
-
Tripos Inc. Sybyl User's Manual Version 7.8; Tripos, Inc., St. Louis, MO, 2002.
-
(2002)
Sybyl User's Manual Version 7.8
-
-
-
23
-
-
0017033395
-
Molecular connectivity VII: Specific treatment of heteroatoms
-
Kier, L. B.; Hall, L. H. Molecular connectivity VII: specific treatment of heteroatoms. J. Pharm. Sci. 1976, 65, 1806-1809.
-
(1976)
J. Pharm. Sci.
, vol.65
, pp. 1806-1809
-
-
Kier, L.B.1
Hall, L.H.2
-
24
-
-
0017133376
-
Molecular connectivity V: Connectivity series concept applied to density
-
Kier, L. B.; Murray, W. J.; Randic, M.: Hall, L. H. Molecular connectivity V: connectivity series concept applied to density. J. Pharm. Sci. 1976, 65, 1226-1230.
-
(1976)
J. Pharm. Sci.
, vol.65
, pp. 1226-1230
-
-
Kier, L.B.1
Murray, W.J.2
Randic, M.3
Hall, L.H.4
-
25
-
-
0016771481
-
Molecular connectivity. 4. Relationships to biological activities
-
Kier, L. B.; Murray, W. J.; Hall, L. H. Molecular connectivity. 4. Relationships to biological activities. J. Med. Chem. 1975, 18, 1272-1274.
-
(1975)
J. Med. Chem.
, vol.18
, pp. 1272-1274
-
-
Kier, L.B.1
Murray, W.J.2
Hall, L.H.3
-
26
-
-
0016771380
-
Molecular connectivity. I: Relationship to nonspecific local anesthesia
-
Kier, L. B.; Hall, L. H.; Murray, W. J.; Randic, M. Molecular connectivity. I: Relationship to nonspecific local anesthesia. J. Pharm. Sci. 1975, 64, 1971-1974.
-
(1975)
J. Pharm. Sci.
, vol.64
, pp. 1971-1974
-
-
Kier, L.B.1
Hall, L.H.2
Murray, W.J.3
Randic, M.4
-
28
-
-
0017100656
-
Molecular connectivity. 6. Examination of the parabolic relationship between molecular connectivity and biological activity
-
Murray, W. J.; Kier, L. B.; Hall, L. H. Molecular connectivity. 6. Examination of the parabolic relationship between molecular connectivity and biological activity. J. Med. Chem. 1976, 19, 573-578.
-
(1976)
J. Med. Chem.
, vol.19
, pp. 573-578
-
-
Murray, W.J.1
Kier, L.B.2
Hall, L.H.3
-
29
-
-
0016830070
-
Molecular connectivity. III: Relationship to partition coefficients
-
Murray, W. J.; Hall, L. H.; Kier, L. B. Molecular connectivity. III: Relationship to partition coefficients. J. Pharm. Sci. 1975, 64, 1978-1981.
-
(1975)
J. Pharm. Sci.
, vol.64
, pp. 1978-1981
-
-
Murray, W.J.1
Hall, L.H.2
Kier, L.B.3
-
30
-
-
5244364312
-
The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding
-
Brown, R. D.; Martin, Y. C. The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding. J. Chem. Inf. Comput. Sci 1997, 37, 1-9.
-
(1997)
J. Chem. Inf. Comput. Sci
, vol.37
, pp. 1-9
-
-
Brown, R.D.1
Martin, Y.C.2
-
31
-
-
11144354205
-
Application of predictive QSAR models to database mining: Identification and experimental validation of novel anticonvulsant compounds
-
Shen, M.; Beguin, C.; Golbraikh, A.; Stables, J. P.; Kohn, H.; Tropsha, A. Application of predictive QSAR models to database mining: identification and experimental validation of novel anticonvulsant compounds. J. Med. Chem. 2004, 47, 2356-2364.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2356-2364
-
-
Shen, M.1
Beguin, C.2
Golbraikh, A.3
Stables, J.P.4
Kohn, H.5
Tropsha, A.6
-
32
-
-
0035003352
-
3-D pharmacophores in drug discovery
-
Mason, J. S.; Good, A. C.; Martin, E. J. 3-D pharmacophores in drug discovery. Curr. Pharm. Des. 2001, 7, 567-597.
-
(2001)
Curr. Pharm. Des.
, vol.7
, pp. 567-597
-
-
Mason, J.S.1
Good, A.C.2
Martin, E.J.3
-
33
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H. Equation of State Calculations by Fast Computing Machines. J. Chem. Phys. 1953, 1087-1092.
-
(1953)
J. Chem. Phys.
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
-
34
-
-
0001565645
-
Cluster analysis by simulated annealing
-
Sun, L.; Xie, Y.; Song, X.; Wang, J.; Yu, R. Cluster Analysis By Simulated Annealing. Comput. Chem. 1994, 103-108.
-
(1994)
Comput. Chem.
, pp. 103-108
-
-
Sun, L.1
Xie, Y.2
Song, X.3
Wang, J.4
Yu, R.5
-
35
-
-
0000378338
-
Novel variable selection quantitative structure-property relationship approach based on the k-nearest-neighbor principle
-
Zheng, W.; Tropsha. A. Novel variable selection quantitative structure-property relationship approach based on the k-nearest-neighbor principle. J. Chem. Inf. Comput. Sci. 2000, 40, 185-194.
-
(2000)
J. Chem. Inf. Comput. Sci.
, vol.40
, pp. 185-194
-
-
Zheng, W.1
Tropsha, A.2
-
36
-
-
0042355453
-
Rational selection of training and test sets for the development of validated QSAR models
-
Golbraikh, A.; Shen, M.; Xiao, Z.; Xiao, Y. D.; Lee, K. H.; Tropsha, A. Rational selection of training and test sets for the development of validated QSAR models. J. Comput.-Aided Mol. Des. 2003, 17, 241-253.
-
(2003)
J. Comput.-aided Mol. Des.
, vol.17
, pp. 241-253
-
-
Golbraikh, A.1
Shen, M.2
Xiao, Z.3
Xiao, Y.D.4
Lee, K.H.5
Tropsha, A.6
-
37
-
-
0036933967
-
Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection
-
Golbraikh, A.; Tropsha, A. Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. Mol. Divers. 2002, 5, 231-243.
-
(2002)
Mol. Divers.
, vol.5
, pp. 231-243
-
-
Golbraikh, A.1
Tropsha, A.2
-
39
-
-
0038724207
-
The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models
-
Tropsha, A.; Gramatica, P.; Gombar, V. K. The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models. Quant. Struct. Act. Relat. Comb. Sci. 2003, 22, 69-77.
-
(2003)
Quant. Struct. Act. Relat. Comb. Sci.
, vol.22
, pp. 69-77
-
-
Tropsha, A.1
Gramatica, P.2
Gombar, V.K.3
|