-
1
-
-
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
-
2
-
-
0009590921
-
Free energy calculations: A breakthrough for modeling organic chemistry in solution
-
Jorgensen, W. L. Free energy calculations: A breakthrough for modeling organic chemistry in solution Acc. Chem. Res. 1989, 22, 184-189
-
(1989)
Acc. Chem. Res.
, vol.22
, pp. 184-189
-
-
Jorgensen, W.L.1
-
3
-
-
77949977626
-
The use of scoring functions in drug discovery applications. in
-
Eds.; Wiley-VCH Inc.: Hoboken, NJ
-
Böhm, H. J.; Stahl, M. The use of scoring functions in drug discovery applications. In Reviews in Computational Chemistry; Lipkowitz, K. B.,; Boyd, D. B., Eds.; Wiley-VCH Inc.: Hoboken, NJ, 2002; Vol. 18, pp 41 - 88.
-
(2002)
Reviews in Computational Chemistry
, vol.18
, pp. 41-88
-
-
Böhm, H.J.1
Stahl, M.2
Lipkowitz, K.B.3
Boyd, D.B.4
-
4
-
-
13444292556
-
Scoring functions for protein-ligand interactions: A critical perspective
-
DOI 10.1016/j.ddtec.2004.08.004, PII S1740674904000149
-
Schulz-Gasch, T.; Stahl, M. Scoring functions for protein-ligand interactions: a critical perspective Drug Discovery Today: Tech. 2004, 1, 231-239 (Pubitemid 40201906)
-
(2004)
Drug Discovery Today: Technologies
, vol.1
, Issue.3
, pp. 231-239
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
5
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
DOI 10.1021/ar000033j
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models Acc. Chem. Res. 2000, 33, 889-897 (Pubitemid 32056774)
-
(2000)
Accounts of Chemical Research
, vol.33
, Issue.12
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
-
6
-
-
84961980685
-
Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinity by a combination of molecular mechanics and continuum solvent models
-
Kuhn, B.; Kollman, P. A. Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinity by a combination of molecular mechanics and continuum solvent models J. Med. Chem. 2000, 43, 3786-3791
-
(2000)
J. Med. Chem.
, vol.43
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
7
-
-
0034212858
-
Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
-
Lee, M. R.; Duan, Y.; Kollman, P. A. Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece Proteins: Struct., Funct., Genet. 2000, 39, 309-316 (Pubitemid 30414169)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.39
, Issue.4
, pp. 309-316
-
-
Lee, M.R.1
Duan, Y.2
Kollman, P.A.3
-
8
-
-
0034257127
-
Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK
-
DOI 10.1002/(SICI)1097-0134(20000801)40:2<185::AID-PROT20>3.0.CO;2- X
-
Kasper, P.; Christen, P.; Gehring, H. Empirical calculations of the relative free energies of peptide binding to the molecular chaperone Dnak Proteins: Struct., Funct., Genet. 2000, 40, 185-192 (Pubitemid 30413623)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.40
, Issue.2
, pp. 185-192
-
-
Kasper, P.1
Christen, P.2
Gehring, H.3
-
9
-
-
33748442331
-
A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method
-
DOI 10.1002/prot.21044
-
Xu, Y.; Wang, R. A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method Proteins: Struct., Funct., Bioinf. 2006, 64, 1058-1068 (Pubitemid 44420944)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.64
, Issue.4
, pp. 1058-1068
-
-
Xu, Y.1
Wang, R.2
-
10
-
-
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
-
11
-
-
33645400172
-
A multistep approach to structure-based drug design: Studying ligand binding at the human neutrophil elastase
-
Steinbrecher, T.; Case, D. A.; Labahn, A. A multistep approach to structure-based drug design: Studying ligand binding at the human neutrophil elastase J. Med. Chem. 2006, 49, 1837-1844
-
(2006)
J. Med. Chem.
, vol.49
, pp. 1837-1844
-
-
Steinbrecher, T.1
Case, D.A.2
Labahn, A.3
-
12
-
-
34547666868
-
Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA
-
Brown, S. P.; Muchmore, S. W. Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA J. Chem. Inf. Model. 2007, 47, 1493-1503
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1493-1503
-
-
Brown, S.P.1
Muchmore, S.W.2
-
13
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
DOI 10.1021/jm049081q
-
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 (Pubitemid 40800612)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.12
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
-
14
-
-
28144441347
-
Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
-
Pearlman, D. A. Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase J. Med. Chem. 2005, 48, 7796-7807
-
(2005)
J. Med. Chem.
, vol.48
, pp. 7796-7807
-
-
Pearlman, D.A.1
-
15
-
-
33750467966
-
Ligand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field
-
DOI 10.1021/jm0608210
-
Weis, A.; Katebzadeh, K.; Soderhjelm, P.; Nilsson, I.; Ryde, U. Ligand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field J. Med. Chem. 2006, 49, 6596-6606 (Pubitemid 44657454)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.22
, pp. 6596-6606
-
-
Weis, A.1
Katebzadeh, K.2
Soderhjelm, P.3
Nilsson, I.4
Ryde, U.5
-
16
-
-
35348864558
-
Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors
-
DOI 10.1016/j.bmc.2007.08.019, PII S0968089607006931
-
Ferrari, A. M.; Degliesposti, G.; Sgobba, M.; Rastelli, G. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors Bioorg. Chem. Med. 2007, 15, 7865-7877 (Pubitemid 47575902)
-
(2007)
Bioorganic and Medicinal Chemistry
, vol.15
, Issue.24
, pp. 7865-7877
-
-
Ferrari, A.M.1
Degliesposti, G.2
Sgobba, M.3
Rastelli, G.4
-
17
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, I. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242; http://www.rcsb.org/pdb/ (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
18
-
-
9944221417
-
Validation of protein structures derived by NMR spectroscopy
-
Spronk, C.; Nabuurs, S. B.; Krieger, E.; Vriend, G.; Vuister, G. W. Validation of protein structures derived by NMR spectroscopy Prog. Nucl. Magn. Reson. Spectrosc. 2004, 45, 315-337
-
(2004)
Prog. Nucl. Magn. Reson. Spectrosc.
, vol.45
, pp. 315-337
-
-
Spronk, C.1
Nabuurs, S.B.2
Krieger, E.3
Vriend, G.4
Vuister, G.W.5
-
19
-
-
2542530042
-
The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
DOI 10.1021/jm030580l
-
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 (Pubitemid 38702694)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.12
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
20
-
-
20444422149
-
The PDBbind database: Methodologies and updates
-
DOI 10.1021/jm048957q
-
Wang, R.; Fang, X.; Lu, Y.; Yang, C. Y.; Wang, S. The PDBbind Database: Methodologies and updates J. Med. Chem. 2005, 48, 4111-4119 (Pubitemid 40800619)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.12
, pp. 4111-4119
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Yang, C.-Y.4
Wang, S.5
-
21
-
-
0033019040
-
Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate
-
Polshakov, V. I.; Birdsall, B.; Frenkiel, T. A.; Gargaro, A. R.; Feeney, J. Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate Protein Sci. 1999, 8, 467-481 (Pubitemid 29117961)
-
(1999)
Protein Science
, vol.8
, Issue.3
, pp. 467-481
-
-
Polshakov, V.I.1
Birdsall, B.2
Frenkiel, T.A.3
Gargaro, A.R.4
Feeney, J.5
-
22
-
-
0034599721
-
Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb
-
Zwahlen, C.; Li, S. C.; Kay, L. E.; Pawson, T.; Forman-Key, J. D. Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb EMBO J. 2000, 19, 1505-1515 (Pubitemid 30182158)
-
(2000)
EMBO Journal
, vol.19
, Issue.7
, pp. 1505-1515
-
-
Zwahlen, C.1
Li, S.-C.2
Kay, L.E.3
Pawson, T.4
Forman-Kay, J.D.5
-
23
-
-
0031790608
-
Structure of a Numb PTB domain-peptide complex suggests a basis for diverse binding specificity
-
DOI 10.1038/4185
-
Li, S. C.; Zwahlen, C.; Vincent, S. J. F.; McGlade, C. J.; Kay, L. E.; Pawson, T.; Forman-Key, J. D. Structure of a Numb PTB domain-peptide complex suggests a basis for diverse binding specificity Nat. Struct. Mol. Biol. 1998, 5, 1075-1083 (Pubitemid 28546271)
-
(1998)
Nature Structural Biology
, vol.5
, Issue.12
, pp. 1075-1083
-
-
Li, S.-C.1
Zwahlen, C.2
Vincent, S.J.F.3
Jane McGlade, C.4
Kay, L.E.5
Pawson, T.6
Forman-Kay, J.D.7
-
24
-
-
0033856956
-
Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics
-
Sich, C.; Improta, S.; Cowley, D. J.; Guenet, C.; Merly, J.-P.; Teufel, M.; Saudek, V. Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics Eur. J. Biochem. 2000, 267, 5342-5354
-
(2000)
Eur. J. Biochem.
, vol.267
, pp. 5342-5354
-
-
Sich, C.1
Improta, S.2
Cowley, D.J.3
Guenet, C.4
Merly, J.-P.5
Teufel, M.6
Saudek, V.7
-
25
-
-
0034730367
-
Structure and specificity of the interaction between the FHA2 domain of rad53 and phosphotyrosyl peptides
-
Wang, P.; Beyon, L. I.-J.; Liao, H.; Beebe, K. D.; Yongkiettrakul, S.; Pei, D.; Tsai, M. D. II. Structure and specificity of the interaction between the FHA2 domain of rad53 and phosphotyrosyl peptides J. Mol. Biol. 2000, 302, 927-940
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 927-940
-
-
Wang, P.1
Beyon, L.I.-J.2
Liao, H.3
Beebe, K.D.4
Yongkiettrakul, S.5
Pei, D.6
Tsai II, M.D.7
-
26
-
-
0035816557
-
2+ Sensitizing Drug EMD 57033
-
DOI 10.1074/jbc.M102418200
-
Wang, X.; Li, M. X.; Spyracopoulos, L.; Beier, N.; Chandra, M.; Solaro, R. J.; Sykes, B. D. Structure of the C-domain of human cardiac troponin C in complex with the Ca2+ sensitizing drug EMD 57033 J. Biol. Chem. 2001, 276, 25456-25466 (Pubitemid 37413035)
-
(2001)
Journal of Biological Chemistry
, vol.276
, Issue.27
, pp. 25456-25466
-
-
Wang, X.1
Li, M.X.2
Spyracopoulos, L.3
Beier, N.4
Chandra, M.5
Solaro, R.J.6
Sykes, B.D.7
-
27
-
-
0037163141
-
147-163 and bepridil
-
DOI 10.1074/jbc.M203896200
-
Wang, X.; Li, M. X.; Sykes, B. D. Structure of the regulatory N-domain of human cardiac troponin C in complex with human cardiac troponin I147-163 and bepridil J. Biol. Chem. 2002, 277, 31124-31133 (Pubitemid 34970818)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.34
, pp. 31124-31133
-
-
Wang, X.1
Li, M.X.2
Sykes, B.D.3
-
28
-
-
0036786190
-
Solution structure of a novel chromoprotein derived from apo-neocarzinostatin and a synthetic chromophore
-
Urbaniak, M. D.; Muskett, F. W.; Finucane, M. D.; Caddick, S.; Woolfson, D. N. Solution structure of a novel chromoprotein derived from apo-neocarzinostatin and a synthetic chromophore Biochemistry 2002, 41, 11731-11739
-
(2002)
Biochemistry
, vol.41
, pp. 11731-11739
-
-
Urbaniak, M.D.1
Muskett, F.W.2
Finucane, M.D.3
Caddick, S.4
Woolfson, D.N.5
-
29
-
-
15744367970
-
Solution NMR structure investigation for releasing mechanism of neocarzinostatin chromophore from the holoprotein
-
DOI 10.1074/jbc.M411579200
-
Takashima, H.; Yoshida, T.; Ishino, T.; Hasuda, K.; Ohkubo, T.; Kobayashi, Y. Solution NMR structure investigation for releasing mechanism of neocarzinostatin chromophore from the holoprotein J. Biol. Chem. 2005, 280, 11340-11346 (Pubitemid 40418441)
-
(2005)
Journal of Biological Chemistry
, vol.280
, Issue.12
, pp. 11340-11346
-
-
Takashima, H.1
Yoshida, T.2
Ishino, T.3
Hasuda, K.4
Ohkubo, T.5
Kobayashi, Y.6
-
30
-
-
0035861991
-
Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope
-
DOI 10.1006/jmbi.2000.5199
-
Pires, J. R.; Taha-Nejad, F.; Toepert, F.; Ast, T.; Hoffmuller, U.; Schneider-Mergener, J.; Kuhne, R.; Macias, M. J.; Oschkinat, H. Solution structures of the YAP65 WW domain and the variant L30K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope J. Mol. Biol. 2001, 314, 1147-1156 (Pubitemid 34073077)
-
(2001)
Journal of Molecular Biology
, vol.314
, Issue.5
, pp. 1147-1156
-
-
Pires, J.R.1
Taha-Nejad, F.2
Toepert, F.3
Ast, T.4
Hoffmuller, U.5
Schneider-Mergener, J.6
Kuhne, R.7
Macias, M.J.8
Oschkinat, H.9
-
31
-
-
0037112758
-
Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules
-
DOI 10.1093/emboj/cdf602
-
Freund, C.; Kuhne, R.; Yang, H. L.; Park, S.; Reinherz, E. L.; Wagner, G. Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules EMBO. J. 2002, 21, 5985-5995 (Pubitemid 35415317)
-
(2002)
EMBO Journal
, vol.21
, Issue.22
, pp. 5985-5995
-
-
Freund, C.1
Kuhne, R.2
Yang, H.3
Park, S.4
Reinherz, E.L.5
Wagner, G.6
-
32
-
-
0348111465
-
Solution Structure and Base Perturbation Studies Reveal a Novel Mode of Alkylated Base Recognition by 3-Methyladenine DNA Glycosylase I
-
DOI 10.1074/jbc.M307500200
-
Cao, C.; Kwon, K.; Jiang, Y. L.; Drohat, A. C.; Stivers, J. T. Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I J. Biol. Chem. 2003, 278, 48012-48020 (Pubitemid 37523251)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.48
, pp. 48012-48020
-
-
Cao, C.1
Kwon, K.2
Jiang, Y.L.3
Drohat, A.C.4
Stivers, J.T.5
-
33
-
-
0142148040
-
The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG
-
DOI 10.1110/ps.03269103
-
Stevens, S. Y.; Cai, S.; Pellecchia, M.; Zuiderweg, E. R. P. The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG Protein Sci. 2003, 12, 2588-2596 (Pubitemid 37310797)
-
(2003)
Protein Science
, vol.12
, Issue.11
, pp. 2588-2596
-
-
Stevens, S.Y.1
Cai, S.2
Pellecchia, M.3
Zuiderweg, E.R.P.4
-
34
-
-
14844299770
-
4A hydrolase
-
DOI 10.1074/jbc.M412318200
-
Swarbrick, J. D.; Buyya, S.; Gunawardana, D.; Gayler, K. R.; McLennan, A. G.; Gooley, P. R. Structure and substrate-binding mechanism of human Ap4A hydrolase J. Biol. Chem. 2005, 280, 8471-8481 (Pubitemid 40349752)
-
(2005)
Journal of Biological Chemistry
, vol.280
, Issue.9
, pp. 8471-8481
-
-
Swarbrick, J.D.1
Buyya, S.2
Gunawardana, D.3
Gayler, K.R.4
McLennan, A.G.5
Gooley, P.R.6
-
35
-
-
36849044219
-
Structure and dynamics of a molten globular enzyme
-
DOI 10.1038/nsmb1325, PII NSMB1325
-
Pervushin, K.; Vamvaca, K.; Vogeli, B.; Hilvert, D. Structure and dynamics of a molten globular enzyme Nat. Struct. Mol. Biol. 2007, 14, 1202-1206 (Pubitemid 350223332)
-
(2007)
Nature Structural and Molecular Biology
, vol.14
, Issue.12
, pp. 1202-1206
-
-
Pervushin, K.1
Vamvaca, K.2
Vogeli, B.3
Hilvert, D.4
-
36
-
-
33751527233
-
Yng1 PHD Finger Binding to H3 Trimethylated at K4 Promotes NuA3 HAT Activity at K14 of H3 and Transcription at a Subset of Targeted ORFs
-
DOI 10.1016/j.molcel.2006.10.026, PII S1097276506007325
-
Taverna, S. D.; Ilin, S.; Rogers, R. S.; Tanny, J. C.; Lavender, H.; Li, H.; Baker, L.; Boyle, J.; Blair, L. P.; Chait, B. T.; Patel, D. J.; Aitchison, J. D.; Tackett, A. J.; Allis, C. D. Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs Mol. Cell 2006, 24, 785-796 (Pubitemid 44839214)
-
(2006)
Molecular Cell
, vol.24
, Issue.5
, pp. 785-796
-
-
Taverna, S.D.1
Ilin, S.2
Rogers, R.S.3
Tanny, J.C.4
Lavender, H.5
Li, H.6
Baker, L.7
Boyle, J.8
Blair, L.P.9
Chait, BrianT.10
Patel, D.J.11
Aitchison, J.D.12
Tackett, A.J.13
Allis, C.D.14
-
37
-
-
35649004472
-
Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3
-
DOI 10.1110/ps.073049407
-
Runyon, S. T.; Zhang, Y.; Appleton, B. A.; Sazinsky, S. L.; Wu, P.; Pan, B.; Wiesmann, C.; Skelton, N. J.; Sidhu, S. S. Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3 Protein Sci. 2007, 16, 2454-2471 (Pubitemid 350036751)
-
(2007)
Protein Science
, vol.16
, Issue.11
, pp. 2454-2471
-
-
Runyon, S.T.1
Zhang, Y.2
Appleton, B.A.3
Sazinsky, S.L.4
Wu, P.5
Pan, B.6
Wiesmann, C.7
Skelton, N.J.8
Sidhu, S.S.9
-
38
-
-
35048854556
-
Structural Characterization of a New Binding Motif and a Novel Binding Mode in Group 2 WW Domains
-
DOI 10.1016/j.jmb.2007.08.052, PII S0022283607011333
-
Ramirez-Espain, X.; Ruiz, L.; Martin-Malpartida, P.; Oschkinat, H.; Macias, M. J. Structural characterization of a new binding motif and a novel binding mode in group 2 WW domains J. Mol. Biol. 2007, 373, 1255-1268 (Pubitemid 47554567)
-
(2007)
Journal of Molecular Biology
, vol.373
, Issue.5
, pp. 1255-1268
-
-
Ramirez-Espain, X.1
Ruiz, L.2
Martin-Malpartida, P.3
Oschkinat, H.4
Macias, M.J.5
-
39
-
-
34648828242
-
Solution structure of the hDlg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 papillomavirus E6 protein
-
DOI 10.1021/bi700879k
-
Liu, Y.; Henry, G. D.; Hegde, R. S.; Baleja, J. D. Solution structure of the hDlg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 Papillomavirus E6 protein Biochemistry 2007, 46, 10864-10874 (Pubitemid 47463038)
-
(2007)
Biochemistry
, vol.46
, Issue.38
, pp. 10864-10874
-
-
Liu, Y.1
Henry, G.D.2
Hegde, R.S.3
Baleja, J.D.4
-
40
-
-
34447261675
-
Structure and Evolutionary Analysis of a Non-biological ATP-binding Protein
-
DOI 10.1016/j.jmb.2007.05.062, PII S0022283607007097
-
Mansy, S. S.; Zhang, J.; Kummerle, R.; Nilsson, M.; Chou, J. J.; Szostak, J. W.; Chaput, J. C. Structure and evolutionary analysis of a non-biological ATP-binding protein J. Mol. Biol. 2007, 371, 501-513 (Pubitemid 47048278)
-
(2007)
Journal of Molecular Biology
, vol.371
, Issue.2
, pp. 501-513
-
-
Mansy, S.S.1
Zhang, J.2
Kummerle, R.3
Nilsson, M.4
Chou, J.J.5
Szostak, J.W.6
Chaput, J.C.7
-
41
-
-
34247186195
-
-
University of California: San Francisco, CA
-
Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9; University of California: San Francisco, CA, 2006.
-
(2006)
AMBER 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Pearlman, D.A.9
Crowley, M.10
Walker, R.C.11
Zhang, W.12
Wang, B.13
Hayik, S.14
Roitberg, A.15
Seabra, G.16
Wong, K.F.17
Paesani, F.18
Wu, X.19
Brozell, S.20
Tsui, V.21
Gohlke, H.22
Yang, L.23
Tan, C.24
Mongan, J.25
Hornak, V.26
Cui, G.27
Beroza, P.28
Mathews, D.H.29
Schafmeister, C.30
Ross, W.S.31
Kollman, P.A.32
more..
-
42
-
-
0038626673
-
-
revision C.02; Gaussian, Inc.: Wallingford, CT
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A. Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
-
(2004)
Gaussian 03
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Montgomery, Jr.J.A.7
Vreven, T.8
Kudin, K.N.9
Burant, J.C.10
Millam, J.M.11
Iyengar, S.S.12
Tomasi, J.13
Barone, V.14
Mennucci, B.15
Cossi, M.16
Scalmani, G.17
Rega, N.18
Petersson, G.A.19
Nakatsuji, H.20
Hada, M.21
Ehara, M.22
Toyota, K.23
Fukuda, R.24
Hasegawa, J.25
Ishida, M.26
Nakajima, T.27
Honda, Y.28
Kitao, O.29
Nakai, H.30
Klene, M.31
Li, X.32
Knox, J.E.33
Hratchian, H.P.34
Cross, J.B.35
Bakken, V.36
Adamo, C.37
Jaramillo, J.38
Gomperts, R.39
Stratmann, R.E.40
Yazyev, O.41
Austin, A.J.42
Cammi, R.43
Pomelli, C.44
Ochterski, J.W.45
Ayala, P.Y.46
Morokuma, K.47
Voth, G.A.48
Salvador, P.49
Dannenberg, J.J.50
Zakrzewski, V.G.51
Dapprich, S.52
Daniels, A.D.53
Strain, M.C.54
Farkas, O.55
Malick, D.K.56
Rabuck, A.D.57
Raghavachari, K.58
Foresman, J.B.59
Ortiz, J.V.60
Cui, Q.61
Baboul, A.G.62
Clifford, S.63
Cioslowski, J.64
Stefanov, B.B.65
Liu, G.66
Liashenko, A.67
Piskorz, P.68
Komaromi, I.69
Martin, R.L.70
Fox, D.J.71
Keith, T.72
Al-Laham, M.A.73
Peng, C.Y.74
Nanayakkara, A.75
Challacombe, M.76
Gill, P.M.W.77
Johnson, B.78
Chen, W.79
Wong, M.W.80
Gonzalez, C.81
Pople, J.A.82
more..
-
43
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model J. Phys. Chem. 1993, 97, 10269-10280
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
44
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
DOI 10.1023/A:1016357811882
-
Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction J. Comput.-Aided Mol. Des. 2002, 16, 11-26 (Pubitemid 34855041)
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.1
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
45
-
-
26444588137
-
CSD-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
-
DOI 10.1021/jm050436v
-
Velec, H. F. G.; Gohlke, H.; Klebe, G. DrugScore(CSD): Knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction J. Med. Chem. 2005, 48, 6296-6303 (Pubitemid 41428984)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.20
, pp. 6296-6303
-
-
Velec, H.F.G.1
Gohlke, H.2
Klebe, G.3
-
46
-
-
0028881193
-
Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
-
Verkhivker, G.; Appelt, K.; Freer, S. T.; Villafranca, J. E. Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity Protein Eng. 1995, 8, 677-691
-
(1995)
Protein Eng.
, vol.8
, pp. 677-691
-
-
Verkhivker, G.1
Appelt, K.2
Freer, S.T.3
Villafranca, J.E.4
-
47
-
-
0033670301
-
Deciphering common failures in molecular docking of ligand-protein complexes
-
Verkhivker, G. M.; Bouzida, D.; Gehlhaar, D. K.; Rejto, P. A.; Arthurs, S.; Rose, P. W. Deciphering common failures in molecular docking of ligand-protein complexes J. Comput.-Aided Mol. Des. 2000, 14, 731-751
-
(2000)
J. Comput.-Aided Mol. Des.
, vol.14
, pp. 731-751
-
-
Verkhivker, G.M.1
Bouzida, D.2
Gehlhaar, D.K.3
Rejto, P.A.4
Arthurs, S.5
Rose, P.W.6
-
48
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes J. Comput.-Aided Mol. Des. 1997, 11, 425-445
-
(1997)
J. Comput.-Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
49
-
-
0032153192
-
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
-
Murray, C. W.; Auton, T. R.; Eldridge, M. D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model J. Comput.-Aided Mol. Des. 1998, 12, 503-519
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 503-519
-
-
Murray, C.W.1
Auton, T.R.2
Eldridge, M.D.3
-
50
-
-
66149103553
-
Comparative assessment of scoring functions on a diverse test set
-
Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative assessment of scoring functions on a diverse test set J. Chem. Inf. Model. 2009, 49, 1079-1093
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1079-1093
-
-
Cheng, T.1
Li, X.2
Li, Y.3
Liu, Z.4
Wang, R.5
-
51
-
-
66149121351
-
Interpretation of the binding affinities of PTP1B inhibitors with the MM-GB/SA method and the X-Score scoring function
-
Zhang, X.; Li, X.; Wang, R. Interpretation of the binding affinities of PTP1B inhibitors with the MM-GB/SA method and the X-Score scoring function J. Chem. Inf. Model. 2009, 49, 1033-1048
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1033-1048
-
-
Zhang, X.1
Li, X.2
Wang, R.3
-
52
-
-
0142246157
-
-
In;, Eds; John Wiley & Sons Inc.: Hoboken, NJ
-
Lamm, G. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Larter, R.; Cundari, T. R., Eds; John Wiley & Sons Inc.: Hoboken, NJ, 2003; Vol. 19, pp 147 - 365.
-
(2003)
Reviews in Computational Chemistry
, vol.19
, pp. 147-365
-
-
Lamm, G.1
Lipkowitz, K.B.2
Larter, R.3
Cundari, T.R.4
-
53
-
-
33750053883
-
-
In;, Eds; John Wiley & Sons Inc.: Hoboken, NJ
-
Baker, N. A. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Larter, R.; Cundari, T. R., Eds; John Wiley & Sons Inc.: Hoboken, NJ, 2005; Vol. 21, pp 349 - 379.
-
(2005)
Reviews in Computational Chemistry
, vol.21
, pp. 349-379
-
-
Baker, N.A.1
Lipkowitz, K.B.2
Larter, R.3
Cundari, T.R.4
-
54
-
-
0033654297
-
Generalized Born Models of Macromolecular Solvation Effects
-
Bashford, D.; Case, D. A. Generalized Born Models of Macromolecular Solvation Effects Annu. Rev. Phys. Chem. 2000, 51, 129-152
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
55
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W. C.; Tempczyk, A.; Hawley, R. C.; 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.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
56
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
DOI 10.1021/ja003834q
-
Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of Efavirenz by docking and MM-PBSA J. Am. Chem. Soc. 2001, 123, 5221-5230 (Pubitemid 32910665)
-
(2001)
Journal of the American Chemical Society
, vol.123
, Issue.22
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
57
-
-
34547887970
-
Theoretical calculation of the binding free energies for pyruvate dehydrogenase E1 binding with ligands
-
DOI 10.1016/j.bmcl.2007.06.095, PII S0960894X07007913
-
Xiong, Y.; Li, Y.; He, H.; Zhan, C. Theoretical calculation of the binding free energies for pyruvate dehydrogenase E1 binding with ligands Bioorg. Med. Chem. Lett. 2007, 17, 5186-5190 (Pubitemid 47259651)
-
(2007)
Bioorganic and Medicinal Chemistry Letters
, vol.17
, Issue.18
, pp. 5186-5190
-
-
Xiong, Y.1
Li, Y.2
He, H.3
Zhan, C.-G.4
-
58
-
-
48749107774
-
Application of a polarizable force field to calculations of relative protein-ligand affinities
-
Khoruzhii, O.; Donchev, A. G.; Galkin, N.; Illarionov, A.; Olevanov, M.; Ozrin, V.; Queen, C.; Tarasov, V. Application of a polarizable force field to calculations of relative protein-ligand affinities Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 10378-10383
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 10378-10383
-
-
Khoruzhii, O.1
Donchev, A.G.2
Galkin, N.3
Illarionov, A.4
Olevanov, M.5
Ozrin, V.6
Queen, C.7
Tarasov, V.8
|