-
2
-
-
77950241221
-
Emerging peptide therapeutics for inflammatory autoimmune diseases
-
Briand J.P., Muller S. (2010) Emerging peptide therapeutics for inflammatory autoimmune diseases. Curr Pharm Des;16:1136-1142.
-
(2010)
Curr Pharm Des
, vol.16
, pp. 1136-1142
-
-
Briand, J.P.1
Muller, S.2
-
4
-
-
77949472320
-
The synergistic use of computation, chemistry and biology to discover novel peptide-based drugs: the time is right
-
Audie J., Boyd C. (2011) The synergistic use of computation, chemistry and biology to discover novel peptide-based drugs: the time is right. Curr Pharm Des;16:567-582.
-
(2011)
Curr Pharm Des
, vol.16
, pp. 567-582
-
-
Audie, J.1
Boyd, C.2
-
5
-
-
33645776269
-
Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain
-
Hou T., Chen K., McLaughlin W.A., Lu B., Wang W. (2006) Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol;2:e1.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Hou, T.1
Chen, K.2
McLaughlin, W.A.3
Lu, B.4
Wang, W.5
-
6
-
-
34247219622
-
Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment
-
Strockbine B., Rizzo R.C. (2007) Binding of antifusion peptides with HIVgp41 from molecular dynamics simulations: quantitative correlation with experiment. Proteins;67:630-642.
-
(2007)
Proteins
, vol.67
, pp. 630-642
-
-
Strockbine, B.1
Rizzo, R.C.2
-
7
-
-
79952164519
-
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking
-
Feliu E., Aloy P., Oliva B. (2011) On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking. Protein Sci;20:529-541.
-
(2011)
Protein Sci
, vol.20
, pp. 529-541
-
-
Feliu, E.1
Aloy, P.2
Oliva, B.3
-
8
-
-
79952132540
-
Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking
-
Pons C., Talavera D., de la Cruz X., Orozco M., Fernandez-Recio J. (2011) Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking. J Chem Inf Model;51:370-377.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 370-377
-
-
Pons, C.1
Talavera, D.2
de la Cruz, X.3
Orozco, M.4
Fernandez-Recio, J.5
-
9
-
-
0029623184
-
Computational methods to predict binding free energy in ligand-receptor complexes
-
Ajay, Murcko M.A. (1995) Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem;38:4953-4967.
-
(1995)
J Med Chem
, vol.38
, pp. 4953-4967
-
-
Ajay Murcko, M.A.1
-
10
-
-
0242443693
-
Force fields for protein simulations
-
Review.
-
Ponder J.W., Case D.A. (2003) Force fields for protein simulations. Adv Protein Chem;66:27-85, Review.
-
(2003)
Adv Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
11
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M. Jr., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc;117:5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
12
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A.D. Jr., Bashford D., Bellott M., Dunbrack R.L. Jr., Evanseck J.D., Field M.J., Fischer S. et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
-
13
-
-
30444448249
-
The GROMOS software for biomolecular simulation: GROMOS05
-
Christen M., Hünenberger P.H., Bakowies D., Baron R., Bürgi R., Geerke D.P., Heinz T.N., Kastenholz M.A., Kräutler V., Oostenbrink C., Peter C., Trzesniak D., van Gunsteren W.F. (2005) The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem;26:1719-1751.
-
(2005)
J Comput Chem
, vol.26
, pp. 1719-1751
-
-
Christen, M.1
Hünenberger, P.H.2
Bakowies, D.3
Baron, R.4
Bürgi, R.5
Geerke, D.P.6
Heinz, T.N.7
Kastenholz, M.A.8
Kräutler, V.9
Oostenbrink, C.10
Peter, C.11
Trzesniak, D.12
van Gunsteren, W.F.13
-
14
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen W.L., Maxwell D.S., Tirado-Rives J. (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc;118:11225-11236.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
15
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski G.A., Friesner R.A., Tirado-Rives J., Jorgensen W.L. (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B;105:6474-6487.
-
(2001)
J Phys Chem B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
16
-
-
0033137131
-
Prediction of the binding energy for small molecules, peptides and proteins
-
Schapira M., Totrov M., Abagyan R. (1999) Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit;12:177-190.
-
(1999)
J Mol Recognit
, vol.12
, pp. 177-190
-
-
Schapira, M.1
Totrov, M.2
Abagyan, R.3
-
17
-
-
0037168045
-
Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics
-
Wang T., Wade R.C. (2002) Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics. J Med Chem;45:4828-4837.
-
(2002)
J Med Chem
, vol.45
, pp. 4828-4837
-
-
Wang, T.1
Wade, R.C.2
-
18
-
-
78751569971
-
Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses
-
Tian F., Yang L., Lv F., Luo X., Pan Y. (2011) Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses. Amino Acids;40:493-503.
-
(2011)
Amino Acids
, vol.40
, pp. 493-503
-
-
Tian, F.1
Yang, L.2
Lv, F.3
Luo, X.4
Pan, Y.5
-
19
-
-
0033523959
-
Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins
-
Rognan D., Lauemoller S.L., Holm A., Buus S., Tschinke V. (1999) Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins. J Med Chem;42:4650-4658.
-
(1999)
J Med Chem
, vol.42
, pp. 4650-4658
-
-
Rognan, D.1
Lauemoller, S.L.2
Holm, A.3
Buus, S.4
Tschinke, V.5
-
20
-
-
80053066016
-
Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function
-
Liao W.W., Arthur J.W. (2011) Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function. PLoS ONE;6:e25055.
-
(2011)
PLoS ONE
, vol.6
-
-
Liao, W.W.1
Arthur, J.W.2
-
21
-
-
34547614501
-
A novel empirical free energy function that explains and predicts protein-protein binding affinities
-
Audie J., Scarlata S. (2007) A novel empirical free energy function that explains and predicts protein-protein binding affinities. Biophys Chem;129:198-211.
-
(2007)
Biophys Chem
, vol.129
, pp. 198-211
-
-
Audie, J.1
Scarlata, S.2
-
22
-
-
57649176930
-
Development and validation of an empirical free energy function for calculating protein-protein binding free energy surfaces
-
Audie J. (2009) Development and validation of an empirical free energy function for calculating protein-protein binding free energy surfaces. Biophys Chem;9:84-91.
-
(2009)
Biophys Chem
, vol.9
, pp. 84-91
-
-
Audie, J.1
-
23
-
-
67349178167
-
Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities
-
Audie J. (2009) Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities. Biophys Chem;143:139-144.
-
(2009)
Biophys Chem
, vol.143
, pp. 139-144
-
-
Audie, J.1
-
24
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl M.J. (1995) Knowledge-based potentials for proteins. Curr Opin Struct Biol;5:229-235.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
25
-
-
2642524483
-
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding
-
Liu S., Zhang C., Zhou H., Zhou Y. (2004) A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins;56:93-101.
-
(2004)
Proteins
, vol.56
, pp. 93-101
-
-
Liu, S.1
Zhang, C.2
Zhou, H.3
Zhou, Y.4
-
26
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
Zhang C., Liu S., Zhu Q., Zhou Y. (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem;48:2325-2335.
-
(2005)
J Med Chem
, vol.48
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.3
Zhou, Y.4
-
27
-
-
73149095625
-
-
Su Y., Zhou A., Xia X., Li W., Sun Z. (2009) Protein Sci;18:2550-2558.
-
(2009)
Protein Sci
, vol.18
, pp. 2550-2558
-
-
Su, Y.1
Zhou, A.2
Xia, X.3
Li, W.4
Sun, Z.5
-
28
-
-
84857428250
-
Prediction of protein-protein binding free energies
-
Vreven T., Hwang H., Pierce B.G., Weng Z. (2012) Prediction of protein-protein binding free energies. Protein Sci;21:396-404.
-
(2012)
Protein Sci
, vol.21
, pp. 396-404
-
-
Vreven, T.1
Hwang, H.2
Pierce, B.G.3
Weng, Z.4
-
29
-
-
80054900286
-
Protein-protein binding affinity prediction on a diverse set of structures
-
Moal I.H., Agius R., Bates P.A. (2011) Protein-protein binding affinity prediction on a diverse set of structures. Bioinformatics;27:3002-3009.
-
(2011)
Bioinformatics
, vol.27
, pp. 3002-3009
-
-
Moal, I.H.1
Agius, R.2
Bates, P.A.3
-
30
-
-
79952177781
-
Protein
-
Kastritis P.L., Moal I.H., Hwang H., Weng Z., Bates P.A., Alexandre M.J.J., Bonvin A.M.J.J., Janin J. (2011) Protein. Science;20:482-491.
-
(2011)
Science
, vol.20
, pp. 482-491
-
-
Kastritis, P.L.1
Moal, I.H.2
Hwang, H.3
Weng, Z.4
Bates, P.A.5
Alexandre, M.J.J.6
Bonvin, A.M.J.J.7
Janin, J.8
-
31
-
-
77950810925
-
New compstatin variants through two de novo protein design frameworks
-
Bellows M.L., Fung H.K., Taylor M.S., Floudas C.A., López de Victoria A., Morikis D. (2010) New compstatin variants through two de novo protein design frameworks. Biophys J;98:2337-2346.
-
(2010)
Biophys J
, vol.98
, pp. 2337-2346
-
-
Bellows, M.L.1
Fung, H.K.2
Taylor, M.S.3
Floudas, C.A.4
López de Victoria, A.5
Morikis, D.6
-
32
-
-
50949117526
-
Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers
-
Hao J., Serohijos A.W., Newton G., Tassone G., Wang Z., Sgroi D.C., Dokholyan N.V., Basilion J.P. (2008) Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers. PLoS Comput Biol;4:e1000138.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Hao, J.1
Serohijos, A.W.2
Newton, G.3
Tassone, G.4
Wang, Z.5
Sgroi, D.C.6
Dokholyan, N.V.7
Basilion, J.P.8
-
33
-
-
81355150680
-
Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping
-
Ben-Shimon A., Niv M.Y. (2011) Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping. PLoS Comput Biol;7:e1002288.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Ben-Shimon, A.1
Niv, M.Y.2
-
34
-
-
0030855775
-
Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine
-
Sleigh S.H., Tame J.R., Dodson E.J., Wilkinson A.J. (1997) Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine. Biochemistry;36:9747-9758.
-
(1997)
Biochemistry
, vol.36
, pp. 9747-9758
-
-
Sleigh, S.H.1
Tame, J.R.2
Dodson, E.J.3
Wilkinson, A.J.4
-
35
-
-
0032806924
-
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes
-
Davies T.G., Hubbard R.E., Tame J.R. (1999) Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci;8:1432-1444.
-
(1999)
Protein Sci
, vol.8
, pp. 1432-1444
-
-
Davies, T.G.1
Hubbard, R.E.2
Tame, J.R.3
-
36
-
-
0032811591
-
Crystallographic and calorimetric analysis of peptide binding to OppA protein
-
Sleigh S.H., Seavers P.R., Wilkinson A.J., Ladbury J.E., Tame J.R. (1999) Crystallographic and calorimetric analysis of peptide binding to OppA protein. J Mol Biol;291:393-415.
-
(1999)
J Mol Biol
, vol.291
, pp. 393-415
-
-
Sleigh, S.H.1
Seavers, P.R.2
Wilkinson, A.J.3
Ladbury, J.E.4
Tame, J.R.5
|