-
1
-
-
0037392942
-
The specificities of protein kinase inhibitors: An update
-
Bain, J.; McLauchlan, H.; Elliott, M.; Cohen, P. The specificities of protein kinase inhibitors: an update. Biochem. J. 2003, 371, 199-204.
-
(2003)
Biochem. J.
, vol.371
, pp. 199-204
-
-
Bain, J.1
McLauchlan, H.2
Elliott, M.3
Cohen, P.4
-
2
-
-
4644248792
-
Recent advances in the design of matrix metalloprotease inhibitors
-
Matter, H.; Schudok, M. Recent advances in the design of matrix metalloprotease inhibitors. Curr. Opin. Drug Discovery Dev. 2004, 7, 513-535.
-
(2004)
Curr. Opin. Drug Discovery Dev.
, vol.7
, pp. 513-535
-
-
Matter, H.1
Schudok, M.2
-
3
-
-
9644303125
-
Naphthamidine urokinase plasminogen activator inhibitors with improved pharmacokinetic properties
-
Bruncko, M.; McClellan, W. J.; Wendt, M. D.; Sauer, D. R.; Geyer, A. et al. Naphthamidine urokinase plasminogen activator inhibitors with improved pharmacokinetic properties. Bioorif. Med. Chem. Lett. 2005, 15, 93-98.
-
(2005)
Bioorif. Med. Chem. Lett.
, vol.15
, pp. 93-98
-
-
Bruncko, M.1
McClellan, W.J.2
Wendt, M.D.3
Sauer, D.R.4
Geyer, A.5
-
4
-
-
0035028658
-
Strategies for the inhibition of serine proteases
-
Walker, B.; Lynas, J. F. Strategies for the inhibition of serine proteases. Cell Mol. Life Sci. 2001, 58, 596-624.
-
(2001)
Cell Mol. Life Sci.
, vol.58
, pp. 596-624
-
-
Walker, B.1
Lynas, J.F.2
-
5
-
-
1542573352
-
The pursuit of differentiated ligands for the glucocorticoid receptor
-
Coghlan, M. J.; Elmore, S. W.; Kym, P. R.; Kort, M. E. The pursuit of differentiated ligands for the glucocorticoid receptor. Curr. Top. Med. Chem. 2003, 3, 1617-1635.
-
(2003)
Curr. Top. Med. Chem.
, vol.3
, pp. 1617-1635
-
-
Coghlan, M.J.1
Elmore, S.W.2
Kym, P.R.3
Kort, M.E.4
-
6
-
-
0035415863
-
Chemogenomic approaches to drug discovery
-
Caron, P. R.; Mullican, M. D.; Mashal, R. D.; Wilson, K. P.; Su, M. S. et al. Chemogenomic approaches to drug discovery. Curr. Opin. Chem. Biol. 2001, 5, 464-470.
-
(2001)
Curr. Opin. Chem. Biol.
, vol.5
, pp. 464-470
-
-
Caron, P.R.1
Mullican, M.D.2
Mashal, R.D.3
Wilson, K.P.4
Su, M.S.5
-
7
-
-
3042724842
-
Computational methods for the identification and optimisation of high quality leads
-
Pirard, B. Computational methods for the identification and optimisation of high quality leads. Comb. Chem. High Throughput Screening 2004, 7, 271-280.
-
(2004)
Comb. Chem. High Throughput Screening
, vol.7
, pp. 271-280
-
-
Pirard, B.1
-
8
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
-
9
-
-
2542586266
-
A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations
-
Rizzo, R. C.; Toba, S.; Kuntz, I. D. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations. J. Med. Chem. 2004, 47, 3065-3074.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3065-3074
-
-
Rizzo, R.C.1
Toba, S.2
Kuntz, I.D.3
-
10
-
-
1442300070
-
Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody
-
Laitinen, T.; Kankare, J. A.; Perakyla, M. Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody. Proteins 2004, 55, 34-43.
-
(2004)
Proteins
, vol.55
, pp. 34-43
-
-
Laitinen, T.1
Kankare, J.A.2
Perakyla, M.3
-
11
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. Validation and use of the MM-PBSA approach for drug discovery. J. Med. Chem. 2005, 48, 4040-4048.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
-
12
-
-
0024491426
-
Recent advances in comparative molecular field analysis (CoMFA)
-
Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. Recent advances in comparative molecular field analysis (CoMFA). Prog. Clin. Biol. Res. 1989, 291, 161-165.
-
(1989)
Prog. Clin. Biol. Res.
, vol.291
, pp. 161-165
-
-
Cramer III, R.D.1
Patterson, D.E.2
Bunce, J.D.3
-
13
-
-
0027944195
-
Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
-
Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem. 1994, 37, 4130-4146.
-
(1994)
J. Med. Chem.
, vol.37
, pp. 4130-4146
-
-
Klebe, G.1
Abraham, U.2
Mietzner, T.3
-
14
-
-
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
-
Bohm, 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, 458-477.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 458-477
-
-
Bohm, M.1
Sturzebecher, J.2
Klebe, G.3
-
15
-
-
15244361633
-
3D-QSAR CoMFA studies on trypsin-like serine protease inhibitors: A comparative selectivity analysis
-
Bhongade, B. A.; Gouripur, V. V.; Gadad, A. K. 3D-QSAR CoMFA studies on trypsin-like serine protease inhibitors: a comparative selectivity analysis. Bioorg. Med. Chem. 2005, 13, 2773-2782.
-
(2005)
Bioorg. Med. Chem.
, vol.13
, pp. 2773-2782
-
-
Bhongade, B.A.1
Gouripur, V.V.2
Gadad, A.K.3
-
16
-
-
0033524009
-
Affinity and selectivity of matrix metalloproteinase inhibitors: A chemometrical study from the perspective of ligands and proteins
-
Matter, H.; Schwab, W. Affinity and selectivity of matrix metalloproteinase inhibitors: a chemometrical study from the perspective of ligands and proteins. J. Med. Chem. 1999, 42, 4506-4523.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 4506-4523
-
-
Matter, H.1
Schwab, W.2
-
17
-
-
0242577782
-
CoMFA and docking study of novel estrogen receptor subtype selective ligands
-
Wolohan, P.; Reichert, D. E. CoMFA and docking study of novel estrogen receptor subtype selective ligands. J. Comput.-Aided Mol. Des. 2003, 17, 313-328.
-
(2003)
J. Comput.-Aided Mol. Des.
, vol.17
, pp. 313-328
-
-
Wolohan, P.1
Reichert, D.E.2
-
18
-
-
0141566733
-
Selectivity fields: Comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors
-
Baskin, I. I.; Tikhonova, I. G.; Palyulin, V. A.; Zefirov, N. S. Selectivity fields: comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors. J. Med. Chem. 2003, 46, 4063-4069.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 4063-4069
-
-
Baskin, I.I.1
Tikhonova, I.G.2
Palyulin, V.A.3
Zefirov, N.S.4
-
19
-
-
0037030707
-
Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: Target family landscapes
-
Naumann, T.; Matter, H. Structural Classification of Protein Kinases Using 3D Molecular Interaction Field Analysis of Their Ligand Binding Sites: Target Family Landscapes. J. Med. Chem. 2002, 45, 2366-2378.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 2366-2378
-
-
Naumann, T.1
Matter, H.2
-
20
-
-
2342636434
-
General model for estimation of the inhibition of protein kinases using Monte Carlo simulations
-
Tominaga, Y.; Jorgensen, W. L. General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. J. Med. Chem. 2004, 47, 2534-2549.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2534-2549
-
-
Tominaga, Y.1
Jorgensen, W.L.2
-
21
-
-
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, 2681 -2691.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
22
-
-
0035979364
-
Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10
-
Kmunicek, J.; Luengo, S.; Gago, F.; Ortiz, A. R.; Wade, R. C. et al. Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. Biochemistry 2001, 40, 8905-8917.
-
(2001)
Biochemistry
, vol.40
, pp. 8905-8917
-
-
Kmunicek, J.1
Luengo, S.2
Gago, F.3
Ortiz, A.R.4
Wade, R.C.5
-
23
-
-
0037168045
-
Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics
-
Wang, T.; Wade, R. C. Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics. J. Med. Chem. 2002, 45, 4828-4837.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 4828-4837
-
-
Wang, T.1
Wade, R.C.2
-
24
-
-
0035866695
-
Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes
-
Wang, T.; Wade, R. C. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. J. Med. Chem. 2001, 44, 961-971.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 961-971
-
-
Wang, T.1
Wade, R.C.2
-
25
-
-
0032510317
-
Comparative binding energy analysis of HIV-1 protease inhibitors: Incorporation of solvent effects and validation as a powerful tool in receptor-based drug design
-
Perez, C.; Pastor, M.; Ortiz, A. R.; Gago, F. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. J. Med. Chem. 1998, 41, 836-852.
-
(1998)
J. Med. Chem.
, vol.41
, pp. 836-852
-
-
Perez, C.1
Pastor, M.2
Ortiz, A.R.3
Gago, F.4
-
26
-
-
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, 805-820.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 805-820
-
-
Murcia, M.1
Ortiz, A.R.2
-
27
-
-
0842304458
-
Serin inhibitors of serine proteases as potential therapeutic agents: The road from thrombin to tryptase to cathepsin G
-
Maryanoff, B. E. Serin inhibitors of serine proteases as potential therapeutic agents: the road from thrombin to tryptase to cathepsin G. J. Med. Chem. 2004, 47, 769-787.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 769-787
-
-
Maryanoff, B.E.1
-
28
-
-
0034470147
-
Sequence determinants of function and evolution in serine proteases
-
Krem, M. M.; Rose, T.; Di Cera, E. Sequence determinants of function and evolution in serine proteases. Trends Cardiovasc. Med. 2000, 10, 171-176.
-
(2000)
Trends Cardiovasc. Med.
, vol.10
, pp. 171-176
-
-
Krem, M.M.1
Rose, T.2
Di Cera, E.3
-
29
-
-
0034632795
-
GRID/CPCA: A new computational tool to design selective ligands
-
Kastenholz, M. A.; Pastor, M.; Cruciani, G.; Haaksma, E. E. J.; Fox, T. GRID/CPCA: A new computational tool to design selective ligands. J. Med. Chem. 2000, 43, 3033-3044.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 3033-3044
-
-
Kastenholz, M.A.1
Pastor, M.2
Cruciani, G.3
Haaksma, E.E.J.4
Fox, T.5
-
30
-
-
0036888650
-
A simple method for visualizing the differences between related receptor sites
-
Sheridan, R. P.; Holloway, M. K.; McGaughey, G.; Mosley, R. T.; Singh, S. B. A simple method for visualizing the differences between related receptor sites. J. Mol. Graphics Modell. 2002, 21, 217-225.
-
(2002)
J. Mol. Graphics Modell.
, vol.21
, pp. 217-225
-
-
Sheridan, R.P.1
Holloway, M.K.2
McGaughey, G.3
Mosley, R.T.4
Singh, S.B.5
-
31
-
-
0031053642
-
Contribution of lysine 60f to S1′ specificity of thrombin
-
Rezaie, A. R.; Olson, S. T. Contribution of lysine 60f to S1′ specificity of thrombin. Biochemistry 1997, 36, 1026-1033.
-
(1997)
Biochemistry
, vol.36
, pp. 1026-1033
-
-
Rezaie, A.R.1
Olson, S.T.2
-
32
-
-
0242410546
-
QSAR study on the affinity of some arylpiperazines towards the 5-HT1A/alpha1-adrenergic receptor using the E-state index
-
Debnath, B.; Samanta, S.; Naskar, S. K.; Roy, K.; Jha, T. QSAR study on the affinity of some arylpiperazines towards the 5-HT1A/alpha1-adrenergic receptor using the E-state index. Bioorg. Med. Chem. Lett. 2003, 13, 2837-2842.
-
(2003)
Bioorg. Med. Chem. Lett.
, vol.13
, pp. 2837-2842
-
-
Debnath, B.1
Samanta, S.2
Naskar, S.K.3
Roy, K.4
Jha, T.5
-
33
-
-
0142124197
-
Receptor-guided alignment-based comparative 3D-QSAR studies of benzylidene malonitrile tyrphostins as EGFR and HER-2 kinase inhibitors
-
Kamath, S.; Buolamwini, J. K. Receptor-guided alignment-based comparative 3D-QSAR studies of benzylidene malonitrile tyrphostins as EGFR and HER-2 kinase inhibitors. J. Med. Chem. 2003, 46, 4657-4668.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 4657-4668
-
-
Kamath, S.1
Buolamwini, J.K.2
-
34
-
-
20244384095
-
Synthesis and three-dimensional quantitative structure-activity relationship analysis of h(3) receptor antagonists containing a neutral heterocyclic polar group
-
Rivara, S.; Mor, M.; Bordi, F.; Silva, C.; Zuliani, V. et al. Synthesis and three-dimensional quantitative structure-activity relationship analysis of h(3) receptor antagonists containing a neutral heterocyclic polar group. Drug Des. Discovery 2003, 18, 65-79.
-
(2003)
Drug Des. Discovery
, vol.18
, pp. 65-79
-
-
Rivara, S.1
Mor, M.2
Bordi, F.3
Silva, C.4
Zuliani, V.5
-
35
-
-
0037011897
-
New serotonin 5-HT(2A), 5-HT(2B), and 5-HT(2C) receptor antagonists: Synthesis, pharmacology, 3D-QSAR, and molecular modeling of (aminoalkyl)benzo and heterocycloalkanones
-
Brea, J.; Rodrigo, J.; Carrieri, A.; Sanz, F.; Cadavid, M. I. et al. New serotonin 5-HT(2A), 5-HT(2B), and 5-HT(2C) receptor antagonists: synthesis, pharmacology, 3D-QSAR, and molecular modeling of (aminoalkyl)benzo and heterocycloalkanones. J. Med. Chem. 2002, 45, 54-71.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 54-71
-
-
Brea, J.1
Rodrigo, J.2
Carrieri, A.3
Sanz, F.4
Cadavid, M.I.5
-
36
-
-
0033918979
-
A 3D-QSAR study on the structural requirements for binding to CB(1) and CB(2) cannabinoid receptors
-
Fichera, M.; Cruciani, G.; Bianchi, A.; Musumarra, G. A 3D-QSAR study on the structural requirements for binding to CB(1) and CB(2) cannabinoid receptors. J. Med. Chem. 2000, 43, 2300-2309.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 2300-2309
-
-
Fichera, M.1
Cruciani, G.2
Bianchi, A.3
Musumarra, G.4
-
37
-
-
84961984929
-
Molecular determinants of MAO selectivity in a series of indolyl-methylamine derivatives: Biological activities, 3D-QSAR/CoMFA analysis, and computational simulation of ligand recognition
-
Moron, J. A.; Campillo, M.; Perez, V.; Unzeta, M.; Pardo, L. Molecular determinants of MAO selectivity in a series of indolyl-methylamine derivatives: biological activities, 3D-QSAR/CoMFA analysis, and computational simulation of ligand recognition. J. Med. Chem. 2000, 43, 1684-1691.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 1684-1691
-
-
Moron, J.A.1
Campillo, M.2
Perez, V.3
Unzeta, M.4
Pardo, L.5
-
38
-
-
0035438389
-
QSARs for 6-azasteroids as inhibitors of human type 1 5alpha-reductase: Prediction of binding affinity and selectivity relative to 3-BHSD
-
Bakken, G. A.; Jurs, P. C. QSARs for 6-azasteroids as inhibitors of human type 1 5alpha-reductase: prediction of binding affinity and selectivity relative to 3-BHSD. J. Chem. Inf. Compuf. Sci. 2001, 41, 1255-1265.
-
(2001)
J. Chem. Inf. Compuf. Sci.
, vol.41
, pp. 1255-1265
-
-
Bakken, G.A.1
Jurs, P.C.2
-
39
-
-
0033614954
-
Conformationally constrained butyrophenones with mixed dopaminergic (D(2)) and serotoninergic (5-HT(2A), 5-HT(2C)) affinities: Synthesis, pharmacology, 3D-QSAR, and molecular modeling of (aminoalkyl)benzo- and -thienocycloalkanones as putative atypical antipsychotics
-
Ravina, E.; Negreira, J.; Cid, J.; Masaguer, C. F.; Rosa, E. et al. Conformationally constrained butyrophenones with mixed dopaminergic (D(2)) and serotoninergic (5-HT(2A), 5-HT(2C)) affinities: synthesis, pharmacology, 3D-QSAR, and molecular modeling of (aminoalkyl)benzo- and -thienocycloalkanones as putative atypical antipsychotics. J. Med. Chem. 1999, 42, 2774-2797.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 2774-2797
-
-
Ravina, E.1
Negreira, J.2
Cid, J.3
Masaguer, C.F.4
Rosa, E.5
-
40
-
-
0032497437
-
γ2 (x = 1-3, 5, and 6)] via comparative molecular field analysis
-
γ2 (x = 1-3, 5, and 6)] via comparative molecular field analysis. J. Med. Chem. 1998, 41, 4130-4142.
-
(1998)
J. Med. Chem.
, vol.41
, pp. 4130-4142
-
-
Huang, Q.1
Liu, R.2
Zhang, P.3
He, X.4
McKernan, R.5
-
41
-
-
19744365702
-
A small molecule-kinase interaction map for clinical kinase inhibitors
-
Fabian, M. A.; Biggs, W. H., III; Treiber, D. K.; Atteridge, C. E.; Azimioara, M. D. et al. A small molecule-kinase interaction map for clinical kinase inhibitors. Nat. Biotechnol. 2005, 23, 329-336.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 329-336
-
-
Fabian, M.A.1
Biggs III, W.H.2
Treiber, D.K.3
Atteridge, C.E.4
Azimioara, M.D.5
-
42
-
-
0004260883
-
-
Molecular Simulations, Inc.: San Diego, CA
-
Insight-II, version 2000; Molecular Simulations, Inc.: San Diego, CA.
-
Insight-II, Version 2000
-
-
-
43
-
-
0026465007
-
Refined 2.3 a X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP, and MQPA, A starting point for improving antithrombotics
-
Brandstetter, H.; Turk, D.; Hoeffken, H. W.; Grosse, D.; Sturzebecher, J. et al. Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP, and MQPA, A starting point for improving antithrombotics. J. Mol. Biol. 1992, 226, 1085-1099.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 1085-1099
-
-
Brandstetter, H.1
Turk, D.2
Hoeffken, H.W.3
Grosse, D.4
Sturzebecher, J.5
-
44
-
-
0025851272
-
Geometry of binding of the N-α-tosylated piperidides of m-amidino-, p-amidino-, and p-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-α-tosylated piperidides of m-amidino-, p-amidino-, and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes. FEBS Lett. 1991, 287, 133-138.
-
(1991)
FEBS Lett.
, vol.287
, pp. 133-138
-
-
Turk, D.1
Sturzebecher, J.2
Bode, W.3
-
45
-
-
0027304964
-
Structure of human des(1-45) factor Xa at 2.2 a resolution
-
Padmanabhan, K.; Padmanabhan, K. P.; Tulinsky, A.; Park, C. H.; Bode, W. et al. Structure of human des(1-45) factor Xa at 2.2 A resolution. J. Mol. Biol. 1993, 232, 947-966.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 947-966
-
-
Padmanabhan, K.1
Padmanabhan, K.P.2
Tulinsky, A.3
Park, C.H.4
Bode, W.5
-
46
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N. et al. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
47
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang, J.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
48
-
-
84986492477
-
Atomic charges derived from semiempirical methods
-
Besler, B. H.; Merz, K. M.; Kollmann, P. A. Atomic charges derived from semiempirical methods. J. Comp. Chem. 1990, 11, 431-439.
-
(1990)
J. Comp. Chem.
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.2
Kollmann, P.A.3
-
49
-
-
0025390935
-
MOPAC: A semiempirical molecular orbital program
-
Stewart, J. J. MOPAC: a semiempirical molecular orbital program. J. Comput.-Aided Mol. Des. 1990, 4, 1-105.
-
(1990)
J. Comput.-Aided Mol. Des.
, vol.4
, pp. 1-105
-
-
Stewart, J.J.1
-
50
-
-
0842341771
-
Development and use of quantum mechanical molecular models. 76. AMI: A new general purpose quantum mechanical molecular model
-
Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. Development and use of quantum mechanical molecular models. 76. 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.P.4
-
51
-
-
25144458667
-
A new progressive-iterative algorithm for multiple structure alignment
-
Lupyan, D.; Leo-Macias, A.; Ortiz, A. R. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 2005, 21, 3255-3263.
-
(2005)
Bioinformatics
, vol.21
, pp. 3255-3263
-
-
Lupyan, D.1
Leo-Macias, A.2
Ortiz, A.R.3
-
52
-
-
0036839162
-
MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
-
Ortiz, A. R.; Strauss, C. E.; Olmea, O. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci. 2002, 11, 2606-2621.
-
(2002)
Protein Sci.
, vol.11
, pp. 2606-2621
-
-
Ortiz, A.R.1
Strauss, C.E.2
Olmea, O.3
-
53
-
-
0004195760
-
-
University of California: San Francisco. CA
-
Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III Wang, J.; Ross, W. S.; Simmerling, C.; Darden, T.; Merz, K. M. Stanton, R. V.; Cheng, A.; Vincent, J. J.; Crowley, M.; Tsui, V. Gohlke, H.; Radmer, R.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. P.; Kollman, A. AMBER 7: University of California: San Francisco. CA.
-
AMBER 7
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Wang, J.5
Ross, W.S.6
Simmerling, C.7
Darden, T.8
Merz, K.M.9
Stanton, R.V.10
Cheng, A.11
Vincent, J.J.12
Crowley, M.13
Tsui, V.14
Gohlke, H.15
Radmer, R.16
Duan, Y.17
Pitera, J.18
Massova, I.19
Seibel, G.L.20
Singh, U.C.21
Weiner, P.P.22
Kollman, A.23
more..
-
54
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B.; Nicholls, A. Classical electrostatics in biology and chemistry. Science 1995, 268, 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
55
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W.; Tempczyk, A.; Hawley, R.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.1
Tempczyk, A.2
Hawley, R.3
Hendrickson, T.4
-
56
-
-
0034227821
-
A general treatment of solvent effects based on screened Coulomb potentials
-
Hassan, S. A.; Guarnieri, F.; Mehler, E. L. A general treatment of solvent effects based on screened Coulomb potentials. J. Phys. Chem. B 2000, 104, 6478-6489.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 6478-6489
-
-
Hassan, S.A.1
Guarnieri, F.2
Mehler, E.L.3
-
57
-
-
0034228977
-
Characterization of hydrogen bonding in a continuum solvent model
-
Hassan, S. A.; Guarnieri, F.; Mehler, E. L. Characterization of hydrogen bonding in a continuum solvent model. J. Phys. Chem. B 2000, 104, 6490-6498.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 6490-6498
-
-
Hassan, S.A.1
Guarnieri, F.2
Mehler, E.L.3
-
58
-
-
0001681052
-
The collinearity problem in linear regression, the partial least squares (PLS) approach to generalized inverses
-
Wold, S.; Ruhe, A.; Wold, H.; Dunn, W. J., III. The collinearity problem in linear regression, the partial least squares (PLS) approach to generalized inverses. SIAM J. Sci. Stat. Comp. 1984, 5, 735-743.
-
(1984)
SIAM J. Sci. Stat. Comp.
, vol.5
, pp. 735-743
-
-
Wold, S.1
Ruhe, A.2
Wold, H.3
Dunn III, W.J.4
|