-
1
-
-
0033178831
-
In silico design for protein stabilization
-
Dahiyat BI. In silico design for protein stabilization. Curr Opin Biotech 1999;10:387-390.
-
(1999)
Curr Opin Biotech
, vol.10
, pp. 387-390
-
-
Dahiyat, B.I.1
-
2
-
-
0032835617
-
De novo design and structural characterization of proteins and metalloproteins
-
DeGrado WF. De novo design and structural characterization of proteins and metalloproteins. Ann Rev Biochem 1999;68:779-819.
-
(1999)
Ann Rev Biochem
, vol.68
, pp. 779-819
-
-
DeGrado, W.F.1
-
4
-
-
0036667734
-
Combinatorial protein design
-
Saven J. Combinatorial protein design. Curr Opin Struct Biol 2002;12:453-458.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 453-458
-
-
Saven, J.1
-
6
-
-
0037954108
-
Prudent modeling of core polar residues in computational protein design
-
Bolon DN, Marcus JS, Ross SA, Mayo SL. Prudent modeling of core polar residues in computational protein design. J Mol Biol 2003;329:611-622.
-
(2003)
J Mol Biol
, vol.329
, pp. 611-622
-
-
Bolon, D.N.1
Marcus, J.S.2
Ross, S.A.3
Mayo, S.L.4
-
7
-
-
0038752617
-
Computational design of receptor and sensor proteins with novel functions
-
Looger LL, Dwyer MA, Smith JJ, Hellinga HW. Computational design of receptor and sensor proteins with novel functions. Nature 2003;423:185-190.
-
(2003)
Nature
, vol.423
, pp. 185-190
-
-
Looger, L.L.1
Dwyer, M.A.2
Smith, J.J.3
Hellinga, H.W.4
-
8
-
-
11844281294
-
A neural network-based method for predicting protein stability changes upon single point mutations
-
Proceedings of the 2004 conference on intelligent systems for molecular biology (ISMB04). New York: Oxford University Press
-
Capriotti E, Fariselli P, Casadio R. A neural network-based method for predicting protein stability changes upon single point mutations. In: Proceedings of the 2004 conference on intelligent systems for molecular biology (ISMB04), Bioinformatics (Suppl. 1), volume 20. New York: Oxford University Press; 2004. p 190-201.
-
(2004)
Bioinformatics (Suppl. 1)
, vol.20
, pp. 190-201
-
-
Capriotti, E.1
Fariselli, P.2
Casadio, R.3
-
9
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
11
-
-
0024442265
-
Free-energy calculatons on protein stability. Thr-157 val-157 mutation of t4 lysozyme
-
Dang LX, Merz KM, Kollman PA. Free-energy calculatons on protein stability. Thr-157 val-157 mutation of t4 lysozyme. J Am Chem Soc 1989;111:8505-8508.
-
(1989)
J Am Chem Soc
, vol.111
, pp. 8505-8508
-
-
Dang, L.X.1
Merz, K.M.2
Kollman, P.A.3
-
12
-
-
0025787845
-
Contribution of the hydrophobic effect to protein stability: Analysis based on simulations of the ile-96-ala mutation in barnsase
-
Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the ile-96-ala mutation in barnsase. Proc Natl Acad Sci USA 1991;88:10880-10884.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 10880-10884
-
-
Prevost, M.1
Wodak, S.J.2
Tidor, B.3
Karplus, M.4
-
13
-
-
0025732376
-
Simulation analysis of the stability mutant r96h of t4 lysozyme
-
Tidor B, Karplus M. Simulation analysis of the stability mutant r96h of t4 lysozyme. Biochemistry 1991;30:3217-3228.
-
(1991)
Biochemistry
, vol.30
, pp. 3217-3228
-
-
Tidor, B.1
Karplus, M.2
-
14
-
-
0026210071
-
Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core
-
Lee C, Levitt M. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature 1991;352:448-451.
-
(1991)
Nature
, vol.352
, pp. 448-451
-
-
Lee, C.1
Levitt, M.2
-
15
-
-
0028075953
-
Protein stability for single substitution mutants and the extent of local compactness in the denatured state
-
Miyazawa S, Jernigan RL. Protein stability for single substitution mutants and the extent of local compactness in the denatured state. Protein Eng 1994;7:1209-1220.
-
(1994)
Protein Eng
, vol.7
, pp. 1209-1220
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
16
-
-
0030348040
-
Testing homology modeling on mutant proteins: Predicting structural and thermodynamic effects in the ala98-val mutants of t4 lysozyme
-
Lee C. Testing homology modeling on mutant proteins: predicting structural and thermodynamic effects in the ala98-val mutants of t4 lysozyme. Fold Des 1995;1:1-12.
-
(1995)
Fold des
, vol.1
, pp. 1-12
-
-
Lee, C.1
-
17
-
-
0034669841
-
Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides
-
Pitera JW, Kollman PA. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Proteins 2000;41:385-397.
-
(2000)
Proteins
, vol.41
, pp. 385-397
-
-
Pitera, J.W.1
Kollman, P.A.2
-
18
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
19
-
-
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
-
Gillis D, 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 1997;272:276-290.
-
(1997)
J Mol Biol
, vol.272
, pp. 276-290
-
-
Gillis, D.1
Rooman, M.2
-
20
-
-
33644841126
-
Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables
-
Topham CM, Srinivasan N, Blundell TL. Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables. Protein Eng 1997;101:46-50.
-
(1997)
Protein Eng
, vol.101
, pp. 46-50
-
-
Topham, C.M.1
Srinivasan, N.2
Blundell, T.L.3
-
21
-
-
0033434366
-
Prediction of stability changes upon single-site mutations using database-derived potentials
-
Gillis D, Rooman M. Prediction of stability changes upon single-site mutations using database-derived potentials. Theor Chem Acc 1999;101:46-50.
-
(1999)
Theor Chem Acc
, vol.101
, pp. 46-50
-
-
Gillis, D.1
Rooman, M.2
-
22
-
-
0035943455
-
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
-
Carter CW, LeFebvre BC, Cammer SA, Torpsha A, Edgell MH. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J Mol Biol 2001;311:625-638.
-
(2001)
J Mol Biol
, vol.311
, pp. 625-638
-
-
Carter, C.W.1
LeFebvre, B.C.2
Cammer, S.A.3
Torpsha, A.4
Edgell, M.H.5
-
23
-
-
0036948069
-
Popmusic, rationally designing point mutations in protein structures
-
Kwasigroch JM, Gillis D, Dehouck Y, Rooman M. Popmusic, rationally designing point mutations in protein structures. Bioinformatics 2002;18:1701-1702.
-
(2002)
Bioinformatics
, vol.18
, pp. 1701-1702
-
-
Kwasigroch, J.M.1
Gillis, D.2
Dehouck, Y.3
Rooman, M.4
-
24
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
25
-
-
0345827721
-
Quantifying the effect of burial of amino acid residues on protein stability
-
Zhou H, Zhou Y. Quantifying the effect of burial of amino acid residues on protein stability. Proteins 2004;54:315-322.
-
(2004)
Proteins
, vol.54
, pp. 315-322
-
-
Zhou, H.1
Zhou, Y.2
-
26
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000;10:139-145.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 139-145
-
-
Lazaridis, T.1
Karplus, M.2
-
27
-
-
0030334742
-
Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory
-
Villegas V, Viguera AR, Aviles FX, Serrano L. Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory. Fold Des 1996;1:29-34.
-
(1996)
Fold des
, vol.1
, pp. 29-34
-
-
Villegas, V.1
Viguera, A.R.2
Aviles, F.X.3
Serrano, L.4
-
28
-
-
0031127043
-
Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: Comparison with zimm-bragg and lifson-roig formalisms
-
Munoz V, Serrano L. Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with zimm-bragg and lifson-roig formalisms. Biopolymers 1997;41:495-509.
-
(1997)
Biopolymers
, vol.41
, pp. 495-509
-
-
Munoz, V.1
Serrano, L.2
-
29
-
-
0032553332
-
Elucidating the folding problem of alpha-helices: Local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters
-
Lacroix E, Viguera AR, Serrano L. Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 1998;284:173-191.
-
(1998)
J Mol Biol
, vol.284
, pp. 173-191
-
-
Lacroix, E.1
Viguera, A.R.2
Serrano, L.3
-
30
-
-
0032834649
-
Experimental verification of the stability profile of mutant protein(spmp) data using mutant human lysozymes
-
Takano K, Ota M, Ogasahara K, Yamagata Y, Nishikawa K, Yutani K. Experimental verification of the stability profile of mutant protein(spmp) data using mutant human lysozymes. Protein Eng 1999;12:663-672.
-
(1999)
Protein Eng
, vol.12
, pp. 663-672
-
-
Takano, K.1
Ota, M.2
Ogasahara, K.3
Yamagata, Y.4
Nishikawa, K.5
Yutani, K.6
-
31
-
-
0034727794
-
Improving the refolding yield of interleukin-4 through the optimization of local interactions
-
Domingues H, Peters J, Schneider KH, Apeler H, Sebald W, Oschkinat H, Serrano L. Improving the refolding yield of interleukin-4 through the optimization of local interactions. J Biotechnol 2000;84:217-230.
-
(2000)
J Biotechnol
, vol.84
, pp. 217-230
-
-
Domingues, H.1
Peters, J.2
Schneider, K.H.3
Apeler, H.4
Sebald, W.5
Oschkinat, H.6
Serrano, L.7
-
32
-
-
0034647415
-
Stabilization of alpha-helices by site-directed mutagenesis reveals the importance of secondary structure in the transition state for acylphosphatase folding
-
Taddei N, Chiti F, Fiaschi T, Bucciantini M, Capanni C, Stefani M. Stabilization of alpha-helices by site-directed mutagenesis reveals the importance of secondary structure in the transition state for acylphosphatase folding. J Mol Biol 2000;300:633-647.
-
(2000)
J Mol Biol
, vol.300
, pp. 633-647
-
-
Taddei, N.1
Chiti, F.2
Fiaschi, T.3
Bucciantini, M.4
Capanni, C.5
Stefani, M.6
-
33
-
-
0035037981
-
Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins?
-
Funahashi J, Takano K, Yutani K. Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins? Protein Eng 2001;14:127-134.
-
(2001)
Protein Eng
, vol.14
, pp. 127-134
-
-
Funahashi, J.1
Takano, K.2
Yutani, K.3
-
34
-
-
4544334447
-
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations
-
Bordner AJ, Abagyan RA. Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Proteins 2004;57:400-413.
-
(2004)
Proteins
, vol.57
, pp. 400-413
-
-
Bordner, A.J.1
Abagyan, R.A.2
-
35
-
-
0029196973
-
Predicting free energy contributions to the conformational stability of folded proteins from the residue sequence with radial basis function networks
-
Casadio R, Compiani M, Fariselli P, Viarelli F. Predicting free energy contributions to the conformational stability of folded proteins from the residue sequence with radial basis function networks. In Proc Int Conf Intell Syst Mol Biol, volume 3, p 81-88, 1995.
-
(1995)
Proc Int Conf Intell Syst Mol Biol
, vol.3
, pp. 81-88
-
-
Casadio, R.1
Compiani, M.2
Fariselli, P.3
Viarelli, F.4
-
36
-
-
16344386178
-
Neural network-based prediction of mutation-induced protein stability changes in staphylococcal nuclease at 20 residue positions
-
Frenz C. Neural network-based prediction of mutation-induced protein stability changes in staphylococcal nuclease at 20 residue positions. Proteins 2005;59:147-151.
-
(2005)
Proteins
, vol.59
, pp. 147-151
-
-
Frenz, C.1
-
37
-
-
0002714543
-
Making large-scale SVM learning practical
-
Schölkopf B, Burges C, Smola A, editors. Cambridge, MA: MIT Press
-
Joachims T. Making large-scale SVM learning practical. Advances in Kernel Methods-Support Vector Learning, In: Schölkopf B, Burges C, Smola A, editors. Cambridge, MA: MIT Press; 1999.
-
(1999)
Advances in Kernel Methods-Support Vector Learning
-
-
Joachims, T.1
-
39
-
-
0029873155
-
Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
-
Gillis D, Rooman M. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J Mol Biol 1996;257:1112-1126.
-
(1996)
J Mol Biol
, vol.257
, pp. 1112-1126
-
-
Gillis, D.1
Rooman, M.2
-
40
-
-
0027169638
-
Improved prediction of protein secondary structure by use of sequence profiles and neural networks
-
Rost B, Sander C. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci USA 1993;90:7558-7562.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 7558-7562
-
-
Rost, B.1
Sander, C.2
-
41
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292;195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
42
-
-
0036568279
-
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
-
Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2001;47:228-235.
-
(2001)
Proteins
, vol.47
, pp. 228-235
-
-
Pollastri, G.1
Przybylski, D.2
Rost, B.3
Baldi, P.4
-
43
-
-
0036568293
-
Prediction of coordination number and relative solvent accessibility in proteins
-
Pollastri G, Baldi P, Fariselli P, Casadio R. Prediction of coordination number and relative solvent accessibility in proteins. Proteins 2001;47:142-153.
-
(2001)
Proteins
, vol.47
, pp. 142-153
-
-
Pollastri, G.1
Baldi, P.2
Fariselli, P.3
Casadio, R.4
-
44
-
-
0033976585
-
Protherm, version 2.0: Thermodynamic database for proteins and mutants
-
Gromiha M, An J, Kono H, Oobatake M, Uedaira H, Prabakaran P, Sarai A. Protherm, version 2.0: thermodynamic database for proteins and mutants. Nucleic Acids Res 2000;28:283-285.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 283-285
-
-
Gromiha, M.1
An, J.2
Kono, H.3
Oobatake, M.4
Uedaira, H.5
Prabakaran, P.6
Sarai, A.7
-
45
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, 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
Weissig, H.6
Shindyalov, I.N.7
-
46
-
-
0043122933
-
Uniqueprot: Creating representative protein-sequence sets
-
Mika S, Rost B. Uniqueprot: creating representative protein-sequence sets. Nucleic Acids Res 2003;31:3789-3791.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3789-3791
-
-
Mika, S.1
Rost, B.2
-
48
-
-
27144489164
-
A tutorial on support vector machines for pattern recognition
-
Burges C. A tutorial on support vector machines for pattern recognition. Knowledge Discovery and Data Mining 1998;2.
-
(1998)
Knowledge Discovery and Data Mining
, pp. 2
-
-
Burges, C.1
-
49
-
-
0003401675
-
A tutorial on support vector regression
-
Royal Holloway College, University of London, UK
-
Smola A, Scholkopf B. A tutorial on support vector regression. In: NeuroCOLT Technical Report NC-TR-98-030. Royal Holloway College, University of London, UK, 1998.
-
(1998)
NeuroCOLT Technical Report NC-TR-98-030
-
-
Smola, A.1
Scholkopf, B.2
-
51
-
-
84899013173
-
Support vector regression machines
-
Petsche T, Mozer MC, Jordan MI, editor. Cambridge, MA; MIT Press
-
Drucker H, Burges CJC, Kaufman L, Smola A, Vapnick V. Support vector regression machines. In Petsche T, Mozer MC, Jordan MI, editor. Advances in neural information processing systems, volume 9. Cambridge, MA; MIT Press, 1997. p 155-161.
-
(1997)
Advances in Neural Information Processing Systems
, vol.9
, pp. 155-161
-
-
Drucker, H.1
Burges, C.J.C.2
Kaufman, L.3
Smola, A.4
Vapnick, V.5
-
52
-
-
0003408420
-
-
Cambridge, MA: MIT Press
-
Scholkopf B, Smola AJ. Learning with kernels: support vector machines, regularization, optimization, and beyond. Cambridge, MA: MIT Press; 2002.
-
(2002)
Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond
-
-
Scholkopf, B.1
Smola, A.J.2
-
53
-
-
33644847339
-
A primer on kernel methods
-
Vert J, Scholkopf B, Tsuda K, editor. Cambridge, MA: MIT press
-
Vert J, Tsuda K, Scholkopf B. A primer on kernel methods. In Vert J, Scholkopf B, Tsuda K, editor. Kernel methods in computational biology. Cambridge, MA: MIT press; 2004. p 55-72.
-
(2004)
Kernel Methods in Computational Biology
, pp. 55-72
-
-
Vert, J.1
Tsuda, K.2
Scholkopf, B.3
-
54
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|