-
2
-
-
0347755642
-
ProTherm, version 4.0: thermodynamic database for proteins and mutants
-
Bava K.A., Gromiha M.M., Uedaira H., Kitajima K., and Sarai A. ProTherm, version 4.0: thermodynamic database for proteins and mutants. Nucleic Acids Res. 32 (2004) D120-D121
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bava, K.A.1
Gromiha, M.M.2
Uedaira, H.3
Kitajima, K.4
Sarai, A.5
-
3
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 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
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
4
-
-
0024578173
-
Free-energy via molecular simulation-applications to chemical and biomolecular systems
-
Beveridge D.L., and Dicapua F.M. Free-energy via molecular simulation-applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18 (1989) 431-492
-
(1989)
Annu. Rev. Biophys. Biophys. Chem.
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
Dicapua, F.M.2
-
5
-
-
4544334447
-
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations
-
Bordner A.J., and Abagyan R.A. Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Proteins 57 (2004) 400-413
-
(2004)
Proteins
, vol.57
, pp. 400-413
-
-
Bordner, A.J.1
Abagyan, R.A.2
-
6
-
-
27544469800
-
Predicting protein stability changes from sequences using support vector machines
-
Capriotti E., Fariselli P., Calabrese R., and Casadio R. Predicting protein stability changes from sequences using support vector machines. Bioinformatics 21 Suppl 2 (2005) ii54-ii58
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
-
-
Capriotti, E.1
Fariselli, P.2
Calabrese, R.3
Casadio, R.4
-
7
-
-
23144461249
-
I-Mutant 2.0: predicting stability changes upon mutation from the protein sequence or structure
-
Capriotti E., Fariselli P., and Casadio R. I-Mutant 2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 33 (2005) W306-W310
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Capriotti, E.1
Fariselli, P.2
Casadio, R.3
-
8
-
-
33644847172
-
Prediction of protein stability changes for single-site mutations using support vector machines
-
Cheng J.L., Randall A., and Baldi P. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62 (2006) 1125-1132
-
(2006)
Proteins
, vol.62
, pp. 1125-1132
-
-
Cheng, J.L.1
Randall, A.2
Baldi, P.3
-
9
-
-
0024442265
-
Free energy calculations on protein stability: Thr-157→Val-157 mutation of T4 lysozyme
-
Dang L.X., Merz M.M., and Kollman P.A. Free energy calculations on protein stability: Thr-157→Val-157 mutation of T4 lysozyme. J. Am. Chem. Soc. 111 (1989) 8505-8508
-
(1989)
J. Am. Chem. Soc.
, vol.111
, pp. 8505-8508
-
-
Dang, L.X.1
Merz, M.M.2
Kollman, P.A.3
-
10
-
-
33746639718
-
Emergence of protein fold families through rational design
-
10.1371/journal.pcbi.0020085 Published online July 7, 2006
-
Ding F., and Dokholyan N.V. Emergence of protein fold families through rational design. PLoS. Comput. Biol. 2 (2006) e85 10.1371/journal.pcbi.0020085 Published online July 7, 2006
-
(2006)
PLoS. Comput. Biol.
, vol.2
-
-
Ding, F.1
Dokholyan, N.V.2
-
11
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y., and Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 (1998) 740-744
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
12
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack R.L., and Cohen F.E. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6 (1997) 1661-1681
-
(1997)
Protein Sci.
, vol.6
, pp. 1661-1681
-
-
Dunbrack, R.L.1
Cohen, F.E.2
-
13
-
-
0038275885
-
High-precision, high-throughput stability determinations facilitated by robotics and a semiautomated titrating fluorometer
-
Edgell M.H., Sims D.A., Pielak G.J., and Yi F. High-precision, high-throughput stability determinations facilitated by robotics and a semiautomated titrating fluorometer. Biochemistry 42 (2003) 7587-7593
-
(2003)
Biochemistry
, vol.42
, pp. 7587-7593
-
-
Edgell, M.H.1
Sims, D.A.2
Pielak, G.J.3
Yi, F.4
-
14
-
-
0021828928
-
Hydrogen-bonding and biological specificity analyzed by protein engineering
-
Fersht A.R., Shi J.P., Knilljones J., Lowe D.M., Wilkinson A.J., Blow D.M., Brick P., Carter P., Waye M.M.Y., and Winter G. Hydrogen-bonding and biological specificity analyzed by protein engineering. Nature 314 (1985) 235-238
-
(1985)
Nature
, vol.314
, pp. 235-238
-
-
Fersht, A.R.1
Shi, J.P.2
Knilljones, J.3
Lowe, D.M.4
Wilkinson, A.J.5
Blow, D.M.6
Brick, P.7
Carter, P.8
Waye, M.M.Y.9
Winter, G.10
-
15
-
-
0026511656
-
The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding
-
Fersht A.R., Matouschek A., and Serrano L. The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224 (1992) 771-782
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
16
-
-
0141748498
-
Energetic and structural analysis of the role of tryptophan 59 in FKBP12
-
Fulton K.F., Jackson S.E., and Buckle A.M. Energetic and structural analysis of the role of tryptophan 59 in FKBP12. Biochemistry 42 (2003) 2364-2372
-
(2003)
Biochemistry
, vol.42
, pp. 2364-2372
-
-
Fulton, K.F.1
Jackson, S.E.2
Buckle, A.M.3
-
17
-
-
0029873155
-
Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
-
Gilis D., and Rooman M. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol. 257 (1996) 1112-1126
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 1112-1126
-
-
Gilis, D.1
Rooman, M.2
-
18
-
-
0030777760
-
Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence
-
Gilis D., and Rooman M. Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol. 272 (1997) 276-290
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 276-290
-
-
Gilis, D.1
Rooman, M.2
-
19
-
-
0034460414
-
PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins
-
Gilis D., and Rooman M. PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. Protein Eng. 13 (2000) 849-856
-
(2000)
Protein Eng.
, vol.13
, pp. 849-856
-
-
Gilis, D.1
Rooman, M.2
-
20
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R., Nielsen J.E., and Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320 (2002) 369-387
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
21
-
-
25844482592
-
Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential
-
Hoppe C., and Schomburg D. Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential. Protein Sci. 14 (2005) 2682-2692
-
(2005)
Protein Sci.
, vol.14
, pp. 2682-2692
-
-
Hoppe, C.1
Schomburg, D.2
-
22
-
-
0025891257
-
Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis
-
Hughson F.M., Barrick D., and Baldwin R.L. Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis. Biochemistry 30 (1991) 4113-4118
-
(1991)
Biochemistry
, vol.30
, pp. 4113-4118
-
-
Hughson, F.M.1
Barrick, D.2
Baldwin, R.L.3
-
23
-
-
0026345750
-
Folding of chymotrypsin inhibitor-2. 1. Evidence for a 2-state transition
-
Jackson S.E., and Fersht A.R. Folding of chymotrypsin inhibitor-2. 1. Evidence for a 2-state transition. Biochemistry 30 (1991) 10428-10435
-
(1991)
Biochemistry
, vol.30
, pp. 10428-10435
-
-
Jackson, S.E.1
Fersht, A.R.2
-
24
-
-
33751120171
-
FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis
-
Khare S.D., Caplow M., and Dokholyan N.V. FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis. Amyloid 13 (2006) 226-235
-
(2006)
Amyloid
, vol.13
, pp. 226-235
-
-
Khare, S.D.1
Caplow, M.2
Dokholyan, N.V.3
-
25
-
-
1242294472
-
Can contact potentials reliably predict stability of proteins?
-
Khatun J., Khare S.D., and Dokholyan N.V. Can contact potentials reliably predict stability of proteins?. J. Mol. Biol. 336 (2004) 1223-1238
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 1223-1238
-
-
Khatun, J.1
Khare, S.D.2
Dokholyan, N.V.3
-
26
-
-
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.H., Chong L., Lee M., Lee T., Duan Y., Wang W., et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33 (2000) 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.H.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
-
27
-
-
0037195144
-
A simple physical model for binding energy hot spots in protein-protein complexes
-
Kortemme T., and Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA 99 (2002) 14116-14121
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14116-14121
-
-
Kortemme, T.1
Baker, D.2
-
28
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman B., and Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. USA 97 (2000) 10383-10388
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
29
-
-
1342324030
-
Exploring folding free energy landscapes using computational protein design
-
Kuhlman B., and Baker D. Exploring folding free energy landscapes using computational protein design. Curr. Opin. Struct. Biol. 14 (2004) 89-95
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 89-95
-
-
Kuhlman, B.1
Baker, D.2
-
30
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T., and Karplus M. Effective energy function for proteins in solution. Proteins Struct. Funct. Genet. 35 (1999) 133-152
-
(1999)
Proteins Struct. Funct. Genet.
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
31
-
-
0025698613
-
Transient folding intermediates characterized by protein engineering
-
Matouschek A., Kellis J.T., Serrano L., Bycroft M., and Fersht A.R. Transient folding intermediates characterized by protein engineering. Nature 346 (1990) 440-445
-
(1990)
Nature
, vol.346
, pp. 440-445
-
-
Matouschek, A.1
Kellis, J.T.2
Serrano, L.3
Bycroft, M.4
Fersht, A.R.5
-
32
-
-
0024292679
-
Site-directed mutagenesis of the cell-binding domain of human fibronectin: separable, synergistic sites mediate adhesive function
-
Obara M., Kang M.S., and Yamada K.M. Site-directed mutagenesis of the cell-binding domain of human fibronectin: separable, synergistic sites mediate adhesive function. Cell 53 (1988) 649-657
-
(1988)
Cell
, vol.53
, pp. 649-657
-
-
Obara, M.1
Kang, M.S.2
Yamada, K.M.3
-
33
-
-
0034788711
-
Knowledge-based potential defined for a rotamer library to design protein sequences
-
Ota M., Isogai Y., and Nishikawa K. Knowledge-based potential defined for a rotamer library to design protein sequences. Protein Eng. 14 (2001) 557-564
-
(2001)
Protein Eng.
, vol.14
, pp. 557-564
-
-
Ota, M.1
Isogai, Y.2
Nishikawa, K.3
-
34
-
-
0024792699
-
Genetic-analysis of protein stability and function
-
Pakula A.A., and Sauer R.T. Genetic-analysis of protein stability and function. Annu. Rev. Genet. 23 (1989) 289-310
-
(1989)
Annu. Rev. Genet.
, vol.23
, pp. 289-310
-
-
Pakula, A.A.1
Sauer, R.T.2
-
35
-
-
33646053131
-
Average assignment method for predicting the stability of protein mutants
-
Saraboji K., Gromiha M.M., and Ponnuswamy M.N. Average assignment method for predicting the stability of protein mutants. Biopolymers 82 (2006) 80-92
-
(2006)
Biopolymers
, vol.82
, pp. 80-92
-
-
Saraboji, K.1
Gromiha, M.M.2
Ponnuswamy, M.N.3
-
36
-
-
12544260150
-
Recapitulation of protein family divergence using flexible backbone protein design
-
Saunders C.T., and Baker D. Recapitulation of protein family divergence using flexible backbone protein design. J. Mol. Biol. 346 (2005) 631-644
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 631-644
-
-
Saunders, C.T.1
Baker, D.2
-
37
-
-
0026553768
-
The folding of an enzyme. 2. Substructure of barnase and the contribution of different interactions to protein stability
-
Serrano L., Kellis J.T., Cann P., Matouschek A., and Fersht A.R. The folding of an enzyme. 2. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224 (1992) 783-804
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 783-804
-
-
Serrano, L.1
Kellis, J.T.2
Cann, P.3
Matouschek, A.4
Fersht, A.R.5
-
38
-
-
0033003955
-
ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
-
Vorobjev Y.N., and Hermans J. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys. Chem. 78 (1999) 195-205
-
(1999)
Biophys. Chem.
, vol.78
, pp. 195-205
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
39
-
-
34249777526
-
Eris: an automated estimator of protein stability
-
Yin S., Ding F., and Dokholyan N.V. Eris: an automated estimator of protein stability. Nat. Methods 4 (2007) 466-467
-
(2007)
Nat. Methods
, vol.4
, pp. 466-467
-
-
Yin, S.1
Ding, F.2
Dokholyan, N.V.3
-
40
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H.Y., and Zhou Y.Q. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11 (2002) 2714-2726
-
(2002)
Protein Sci.
, vol.11
, pp. 2714-2726
-
-
Zhou, H.Y.1
Zhou, Y.Q.2
|