-
1
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L. Assessing scoring functions for protein-ligand interactions. J. Med. Chem. 2004, 47 (12), 3032-3047.
-
(2004)
J. Med. Chem
, vol.47
, Issue.12
, pp. 3032-3047
-
-
Ferrara, P.1
Gohlke, H.2
Price, D.J.3
Klebe, G.4
Brooks, C.L.5
-
2
-
-
0242677271
-
Quantitative Approach to Biochemical Structure-Activity Relationships
-
Hansch, C. A Quantitative Approach to Biochemical Structure-Activity Relationships. Acc. Chem. Res. 1969,2, 232-239.
-
(1969)
Acc. Chem. Res
, vol.2
, pp. 232-239
-
-
Hansch, C.A.1
-
3
-
-
0023751431
-
Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins
-
Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
-
(1988)
J. Am. Chem. Soc
, vol.110
, pp. 5959-5967
-
-
Cramer III, R.D.1
Patterson, D.E.2
Bunce, J.D.3
-
4
-
-
0002207845
-
Comparative binding energy analysis
-
Wade, R. C.; Ortiz, A. R.; Gago, F., Comparative binding energy analysis. Perspect. Drug Discovery Des. 1998, 9-11, 19-34.
-
(1998)
Perspect. Drug Discovery Des
, vol.9-11
, pp. 19-34
-
-
Wade, R.C.1
Ortiz, A.R.2
Gago, F.3
-
5
-
-
0029000922
-
Prediction of Drug-Binding Affinities by Comparative Binding-Energy Analysis
-
Ortiz, a. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of Drug-Binding Affinities by Comparative Binding-Energy Analysis. J. Med. Chem. 1995, 38 (14), 2681-2691.
-
(1995)
J. Med. Chem
, vol.38
, Issue.14
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
6
-
-
84961980685
-
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of their Relative Affinites by Combination of Molecular Mechanics and Continuum Solvation Models
-
Kuhn, B.; Kollman, P. A. Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of their Relative Affinites by Combination of Molecular Mechanics and Continuum Solvation Models. J. Med. Chem. 2000, 43 (20), 3786-3791.
-
(2000)
J. Med. Chem
, vol.43
, Issue.20
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
7
-
-
0034789590
-
An Analysis of the Interactions between the Sem-5 SH3 Domain and its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis
-
Wang, W.; Lim, W. A.; Jakalian, A.; Wang, J.; Wang, J.; Luo, R.; Bayly, C. I.; Kollman, P. A., An Analysis of the Interactions between the Sem-5 SH3 Domain and its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis. J. Am. Chem. Soc. 2001, 123, 3986-3994.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 3986-3994
-
-
Wang, W.1
Lim, W.A.2
Jakalian, A.3
Wang, J.4
Wang, J.5
Luo, R.6
Bayly, C.I.7
Kollman, P.A.8
-
8
-
-
0035965479
-
Some recent developments in PLS modeling
-
Wold, S.; Trygg, J.; Berglund, A.; Antti, H. Some recent developments in PLS modeling. Chemom. Intell. Lab. Syst. 2001, 58 (2), 131-150.
-
(2001)
Chemom. Intell. Lab. Syst
, vol.58
, Issue.2
, pp. 131-150
-
-
Wold, S.1
Trygg, J.2
Berglund, A.3
Antti, H.4
-
9
-
-
0035965476
-
PLS-regression: A basic tool of chemometrics
-
Wold, S.; Sjostrom, M.; Eriksson, L. PLS-regression: a basic tool of chemometrics. Chemom. Intell. Lab. Syst. 2001, 58 (2), 109-130.
-
(2001)
Chemom. Intell. Lab. Syst
, vol.58
, Issue.2
, pp. 109-130
-
-
Wold, S.1
Sjostrom, M.2
Eriksson, L.3
-
11
-
-
0001499720
-
Linear Scaling Molecular Orbital Calculations of Biological Systems Using the Semiempirical Divide and Conquer Method
-
van der Vaart, A.; Gogonea, V.; Dixon, S. L.; Merz, K. M., Jr. Linear Scaling Molecular Orbital Calculations of Biological Systems Using the Semiempirical Divide and Conquer Method. J. Comput. Chem. 2000, 21, 1494-1504.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1494-1504
-
-
van der Vaart, A.1
Gogonea, V.2
Dixon, S.L.3
Merz Jr., K.M.4
-
12
-
-
0346506503
-
Accurate Semiempirical Molecular Orbital Calculations for Macromolecules
-
Dixon, S. L.; Merz, K. M., Jr. Fast, Accurate Semiempirical Molecular Orbital Calculations for Macromolecules. J. Chem. Phys. 1997, 107, 879-893.
-
(1997)
J. Chem. Phys
, vol.107
, pp. 879-893
-
-
Dixon, S.L.1
Merz, K.2
Fast Jr., M.3
-
13
-
-
4143104515
-
Semiempirical Molecular Orbital Calculations with Linear System Size Scaling
-
Dixon, S. L.; Merz, K. M., Jr. Semiempirical Molecular Orbital Calculations with Linear System Size Scaling. J. Chem. Phys. 1996, 104, 6643-6649.
-
(1996)
J. Chem. Phys
, vol.104
, pp. 6643-6649
-
-
Dixon, S.L.1
Merz Jr., K.M.2
-
14
-
-
0043144732
-
-
Yang, W.; Lee, T.-S. A Density-matrix Divide-and-conquer Approach for Electronic Structure Calculations of Large Molecules. J. Chem. Phys. 1995, 103 (13), 5674-5678.
-
Yang, W.; Lee, T.-S. A Density-matrix Divide-and-conquer Approach for Electronic Structure Calculations of Large Molecules. J. Chem. Phys. 1995, 103 (13), 5674-5678.
-
-
-
-
15
-
-
35949007371
-
Density-Matrix Electronic-Structure Method with Linear System-Size Scaling
-
Li, X. P.; Nunes, R. W.; Vanderbilt, D. Density-Matrix Electronic-Structure Method with Linear System-Size Scaling. Phys. Rev. B 1993, 47 (16), 10891-10894.
-
(1993)
Phys. Rev. B
, vol.47
, Issue.16
, pp. 10891-10894
-
-
Li, X.P.1
Nunes, R.W.2
Vanderbilt, D.3
-
16
-
-
0001131626
-
Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations
-
Stewart, J. J. P. Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations. Int. J. Quantum Chem. 1996, 58 (2), 133-146.
-
(1996)
Int. J. Quantum Chem
, vol.58
, Issue.2
, pp. 133-146
-
-
Stewart, J.J.P.1
-
17
-
-
0003463895
-
-
The Pennsylvania State University
-
Dixon, S. L.; van der Vaart, A.; Gogonea, V.; Vincent, J. J.; Brothers, E. N.; Suárez, D.; Westerhoff, L. M.; Merz, K. M., Jr. DIVCON99, The Pennsylvania State University: 1999.
-
(1999)
DIVCON99
-
-
Dixon, S.L.1
van der Vaart, A.2
Gogonea, V.3
Vincent, J.J.4
Brothers, E.N.5
Suárez, D.6
Westerhoff, L.M.7
Merz Jr., K.M.8
-
18
-
-
0842341771
-
A New General Purpose Quantum Mechanical Molecular Model
-
Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AMI: A New General Purpose Quantum Mechanical Molecular Model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
-
(1985)
J. Am. Chem. Soc
, vol.107
, pp. 3902-3909
-
-
Dewar, M.J.S.1
Zoebisch, E.G.2
Healy, E.F.3
Stewart, J.J.4
AMI, P.5
-
19
-
-
84988129057
-
-
Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods I. Method: J. Comput. Chem. 1989, 10, 209-220.
-
Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods I. Method: J. Comput. Chem. 1989, 10, 209-220.
-
-
-
-
20
-
-
84988073214
-
Optimization of Parameters for Semiempirical Methods II. Applications
-
Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods II. Applications. J. Comput. Chem. 1989, 10, 221-264.
-
(1989)
J. Comput. Chem
, vol.10
, pp. 221-264
-
-
Stewart, J.J.P.1
-
21
-
-
0038762283
-
Extension of MNDO to d Orbitals: Parameters and Results for the Second-Row Elements and for the Zinc Group
-
Thiel, W.; Voityuk, A. A. Extension of MNDO to d Orbitals: Parameters and Results for the Second-Row Elements and for the Zinc Group. J. Phys. Chem. 1996, 100, 616-626.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 616-626
-
-
Thiel, W.1
Voityuk, A.A.2
-
22
-
-
24444468650
-
Ground States of Molecules. 38. The MNDO method. Approximations and Parameters
-
Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 38. The MNDO method. Approximations and Parameters. J. Am. Chem. Soc. 1977, 99 (15), 4899-4907.
-
(1977)
J. Am. Chem. Soc
, vol.99
, Issue.15
, pp. 4899-4907
-
-
Dewar, M.J.S.1
Thiel, W.2
-
23
-
-
0036889839
-
PDDG/ PM3 and PDDG/MNDO: Improved semiempirical methods
-
Repasky, M. P.; Chandrasekhar, J.; Jorgensen, W. L. PDDG/ PM3 and PDDG/MNDO: Improved semiempirical methods. J. Comput. Chem. 2002, 23 (16), 1601-1622.
-
(2002)
J. Comput. Chem
, vol.23
, Issue.16
, pp. 1601-1622
-
-
Repasky, M.P.1
Chandrasekhar, J.2
Jorgensen, W.L.3
-
24
-
-
0942276314
-
A Quantum Mechanics Based Scoring Function: Study of Zinc-ion Mediated Ligand Binding
-
Raha, K.; Merz, K. M., Jr. A Quantum Mechanics Based Scoring Function: Study of Zinc-ion Mediated Ligand Binding. J. Am. Chem. Soc. 2004, 126, 1020-1021.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 1020-1021
-
-
Raha, K.1
Merz Jr., K.M.2
-
25
-
-
22244451417
-
Large-scale validation of a quantum mechanics based scoring function: Predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes
-
Raha, K.; Merz, K. M., Jr. Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J. Med. Chem. 2005, 48 (14), 4558-75.
-
(2005)
J. Med. Chem
, vol.48
, Issue.14
, pp. 4558-4575
-
-
Raha, K.1
Merz Jr., K.M.2
-
26
-
-
18644382069
-
Pairwise Decomposition of Residue Interaction Energies Using Semiempirical Quantum Mechanical Methods in Studies of Protein-Ligand Interaction
-
Raha, K.; van der Vaart, A. J.; Riley, K. E.; Peters, M. B.; Westerhoff, L. M.; Kim, H.; Merz, K. M., Jr. Pairwise Decomposition of Residue Interaction Energies Using Semiempirical Quantum Mechanical Methods in Studies of Protein-Ligand Interaction. J. Am. Chem. Soc. 2005, 127 (18), 6583-6594.
-
(2005)
J. Am. Chem. Soc
, vol.127
, Issue.18
, pp. 6583-6594
-
-
Raha, K.1
van der Vaart, A.J.2
Riley, K.E.3
Peters, M.B.4
Westerhoff, L.M.5
Kim, H.6
Merz Jr., K.M.7
-
27
-
-
4544344685
-
Pose Scoring by NMR
-
Wang, B.; Raha, K.; Merz, K. M., Jr. Pose Scoring by NMR. J. Am. Chem. Soc. 2004, 126 (37), 11430-11431.
-
(2004)
J. Am. Chem. Soc
, vol.126
, Issue.37
, pp. 11430-11431
-
-
Wang, B.1
Raha, K.2
Merz Jr., K.M.3
-
28
-
-
0026337077
-
The Coagulation Cascade - Initiation, Maintenance, and Regulation
-
Davie, E. W.; Fujikawa, K.; Kisiel, W. The Coagulation Cascade - Initiation, Maintenance, and Regulation. Biochemistry 1991, 30 (43), 10363-10370.
-
(1991)
Biochemistry
, vol.30
, Issue.43
, pp. 10363-10370
-
-
Davie, E.W.1
Fujikawa, K.2
Kisiel, W.3
-
30
-
-
0025851272
-
Geometry of Binding of the N-Alpha-Tosylated Piperidides of Meta-Amidino-Phenylalanine, Para-Amidino-Phenylalanine and Para-Guanidino-Phenylalanine to Thrombin and Trypsin - X-ray Crystal-Structures of Their Trypsin Complexes and Modeling of Their Thrombin Complexes
-
Turk, D.; Sturzebecher, J.; Bode, W. Geometry of Binding of the N-Alpha-Tosylated Piperidides of Meta-Amidino-Phenylalanine, Para-Amidino-Phenylalanine and Para-Guanidino-Phenylalanine to Thrombin and Trypsin - X-ray Crystal-Structures of Their Trypsin Complexes and Modeling of Their Thrombin Complexes. FEBS Lett. 1991, 287 (1-2), 133-138.
-
(1991)
FEBS Lett
, vol.287
, Issue.1-2
, pp. 133-138
-
-
Turk, D.1
Sturzebecher, J.2
Bode, W.3
-
31
-
-
0035955550
-
Factorising ligand affinity: A combined thermodynamic and crystallographic study of trypsin and thrombin inhibition
-
Dullweber, F.; Stubbs, M. T.; Musil, D.; Sturzebecher, J.; Klebe, G. Factorising ligand affinity: A combined thermodynamic and crystallographic study of trypsin and thrombin inhibition. J. Mol. Biol. 2001, 313 (3), 593-614.
-
(2001)
J. Mol. Biol
, vol.313
, Issue.3
, pp. 593-614
-
-
Dullweber, F.1
Stubbs, M.T.2
Musil, D.3
Sturzebecher, J.4
Klebe, G.5
-
32
-
-
0000705433
-
Studies on the active center of trypsin; the binding of amidines and guanidines as models of the substrate side chain
-
Mares-Guia, M.; Shaw, E. Studies on the active center of trypsin; the binding of amidines and guanidines as models of the substrate side chain. J. Biol. Chem. 1965, 240, 1579-1585.
-
(1965)
J. Biol. Chem
, vol.240
, pp. 1579-1585
-
-
Mares-Guia, M.1
Shaw, E.2
-
33
-
-
0030768740
-
Synthesis and structure-activity relationships of potent thrombin inhibitors: Piperazides of 3-amidinophenylalanine
-
Sturzebecher, J.; Prasa, D.; Hauptmann, J.; Vieweg, H.; Wilkstrom, P. Synthesis and structure-activity relationships of potent thrombin inhibitors: Piperazides of 3-amidinophenylalanine. J. Med. Chem. 1997, 40 (19), 3091-3099.
-
(1997)
J. Med. Chem
, vol.40
, Issue.19
, pp. 3091-3099
-
-
Sturzebecher, J.1
Prasa, D.2
Hauptmann, J.3
Vieweg, H.4
Wilkstrom, P.5
-
34
-
-
0028933176
-
Structure-Activity-Relationships of Inhibitors Derived from 3- Amidinophenylalanine
-
Sturzebecher, J.; Prasa, D.; Wikstrom, P.; Vieweg, H. Structure-Activity-Relationships of Inhibitors Derived from 3- Amidinophenylalanine. J. Enzymol. Inhib. 1995, 9 (1), 87-99.
-
(1995)
J. Enzymol. Inhib
, vol.9
, Issue.1
, pp. 87-99
-
-
Sturzebecher, J.1
Prasa, D.2
Wikstrom, P.3
Vieweg, H.4
-
35
-
-
0037920567
-
Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa
-
Böhm, M.; Sturzebecher, J.; Klebe, G. Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa. J. Med. Chem. 1999, 42 (3), 458-477.
-
(1999)
J. Med. Chem
, vol.42
, Issue.3
, pp. 458-477
-
-
Böhm, M.1
Sturzebecher, J.2
Klebe, G.3
-
36
-
-
0542451678
-
Comparative Molecular Similarity Indices: CoMSIA
-
Kubinyi, H, Folkers, G, Martin, Y. C, Eds, Kluwer Academic Publishers: Great Britain
-
Klebe, G. Comparative Molecular Similarity Indices: CoMSIA. In 3D QSAR in Drug Design; Kubinyi, H., Folkers, G., Martin, Y. C., Eds.; Kluwer Academic Publishers: Great Britain, 1998; Vol. 3, p 87.
-
(1998)
3D QSAR in Drug Design
, vol.3
, pp. 87
-
-
Klebe, G.1
-
37
-
-
0034325196
-
Quantum similarity QSAR: Study of inhibitors binding to thrombin, trypsin and factor Xa, including a comparison with CoMFA and CoMSIA methods
-
Robert, D.; Amat, L.; Carbo-Dorca, R. Quantum similarity QSAR: Study of inhibitors binding to thrombin, trypsin and factor Xa, including a comparison with CoMFA and CoMSIA methods. Int. J. Quantum Chem. 2000, 80 (3), 265-282.
-
(2000)
Int. J. Quantum Chem
, vol.80
, Issue.3
, pp. 265-282
-
-
Robert, D.1
Amat, L.2
Carbo-Dorca, R.3
-
38
-
-
0842304437
-
Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors
-
Murcia, M.; Ortiz, A. R. Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors. J. Med. Chem. 2004, 47 (4), 805-820.
-
(2004)
J. Med. Chem
, vol.47
, Issue.4
, pp. 805-820
-
-
Murcia, M.1
Ortiz, A.R.2
-
39
-
-
0029011701
-
-
Cornell, W. D.; Cieplak, P.; Baylay, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
Cornell, W. D.; Cieplak, P.; Baylay, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
-
-
-
40
-
-
33846249746
-
-
R R: A Language and Environment for Statistical Computing, 2.0.1; R Development Core Team: R Foundation for Statistical Computing: Vienna, Austria, 2005.
-
R R: A Language and Environment for Statistical Computing, 2.0.1; R Development Core Team: R Foundation for Statistical Computing: Vienna, Austria, 2005.
-
-
-
-
41
-
-
16244390208
-
Mean squared error of prediction (MSEP) estimates for principal component regression (PCR) and partial least squares regression (PLSR)
-
Mevik, B. H.; Cederkvist, H. R. Mean squared error of prediction (MSEP) estimates for principal component regression (PCR) and partial least squares regression (PLSR). J. Chemom. 2004, 18 (9), 422-429.
-
(2004)
J. Chemom
, vol.18
, Issue.9
, pp. 422-429
-
-
Mevik, B.H.1
Cederkvist, H.R.2
-
42
-
-
0036864322
-
Robust fuzzy principal component analysis (FPCA). A comparative study concerning interaction of carbon-hydrogen bonds with molybdenumoxo bonds
-
Cundari, T. R.; Sarbu, C.; Pop, H. F. Robust fuzzy principal component analysis (FPCA). A comparative study concerning interaction of carbon-hydrogen bonds with molybdenumoxo bonds. J. Chem. Inf. Comput. Sci. 2002, 42 (6), 1363-1369.
-
(2002)
J. Chem. Inf. Comput. Sci
, vol.42
, Issue.6
, pp. 1363-1369
-
-
Cundari, T.R.1
Sarbu, C.2
Pop, H.F.3
-
43
-
-
0036006911
-
Beware of q(2)!
-
Golbraikh, A.; Tropsha, a., Beware of q(2)! J. Mol. Graphics 2002, 20, (4), 269-276.
-
(2002)
J. Mol. Graphics
, vol.20
, Issue.4
, pp. 269-276
-
-
Golbraikh, A.1
Tropsha, A.2
-
44
-
-
0141890762
-
On the physical interpretation of QSAR models
-
Stanton, D. T. On the physical interpretation of QSAR models. J. Chem. Inf. Comput. Sci. 2003, 43 (5), 1423-1433.
-
(2003)
J. Chem. Inf. Comput. Sci
, vol.43
, Issue.5
, pp. 1423-1433
-
-
Stanton, D.T.1
|