-
1
-
-
19544385993
-
CoC: A database of universally conserved residues in protein folds
-
Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, Mirny LA. CoC: a database of universally conserved residues in protein folds. Bioinformatics 2005;21:2539-2540.
-
(2005)
Bioinformatics
, vol.21
, pp. 2539-2540
-
-
Donald, J.E.1
Hubner, I.A.2
Rotemberg, V.M.3
Shakhnovich, E.I.4
Mirny, L.A.5
-
2
-
-
0037382258
-
Atom depth as a descriptor of the protein interior
-
Pintar A, Carugo O, Pongor S. Atom depth as a descriptor of the protein interior. Biophys J 2003;84:2553-2561.
-
(2003)
Biophys J
, vol.84
, pp. 2553-2561
-
-
Pintar, A.1
Carugo, O.2
Pongor, S.3
-
3
-
-
0025729007
-
A nuclear-magnetic-resonance study of the hydrogen-exchange behavior of lysozyme in crystals and solution
-
Pedersen TG, Sigurskjold BW, Andersen KV, Kjaer M, Poulsen FM, Dobson CM, Redfield C. A nuclear-magnetic-resonance study of the hydrogen-exchange behavior of lysozyme in crystals and solution. J Mol Biol 1991;218:413-426.
-
(1991)
J Mol Biol
, vol.218
, pp. 413-426
-
-
Pedersen, T.G.1
Sigurskjold, B.W.2
Andersen, K.V.3
Kjaer, M.4
Poulsen, F.M.5
Dobson, C.M.6
Redfield, C.7
-
4
-
-
0033565815
-
Residue depth: A novel parameter for the analysis of protein structure and stability
-
Chakravarty S, Varadarajan R. Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 1999;7:723-732.
-
(1999)
Structure
, vol.7
, pp. 723-732
-
-
Chakravarty, S.1
Varadarajan, R.2
-
5
-
-
0042674397
-
Using a neural network and spatial clustering to predict the location of active sites in enzymes
-
Gutteridge A, Bartlett GJ, Thornton JM. Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol 2003;330:719-734.
-
(2003)
J Mol Biol
, vol.330
, pp. 719-734
-
-
Gutteridge, A.1
Bartlett, G.J.2
Thornton, J.M.3
-
6
-
-
2542631929
-
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
-
Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004;55:1005-1013.
-
(2004)
Proteins
, vol.55
, pp. 1005-1013
-
-
Zhou, H.1
Zhou, Y.2
-
8
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee B, Richards F. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
-
(1971)
J Mol Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.2
-
9
-
-
33750165508
-
Atom-wise statistics and prediction of solvent accessibility in proteins
-
Singh YH, Gromiha MM, Sarai A, Ahmad S. Atom-wise statistics and prediction of solvent accessibility in proteins. Biophys Chem 2006;124:145-154.
-
(2006)
Biophys Chem
, vol.124
, pp. 145-154
-
-
Singh, Y.H.1
Gromiha, M.M.2
Sarai, A.3
Ahmad, S.4
-
10
-
-
0028109886
-
Conservation and prediction of solvent accessibility in protein families
-
Rost B, Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins 1994;20:216-226.
-
(1994)
Proteins
, vol.20
, pp. 216-226
-
-
Rost, B.1
Sander, C.2
-
11
-
-
0029885547
-
Predicting solvent accessibility: Higher accuracy using Bayesian statistics and optimized residue substitution classes
-
Thompson MJ, Goldstein RA. Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes. Proteins 1996;25:38-47.
-
(1996)
Proteins
, vol.25
, pp. 38-47
-
-
Thompson, M.J.1
Goldstein, R.A.2
-
12
-
-
0033768867
-
Predicting residue solvent accessibility from protein sequence by considering the sequence environment
-
Carugo O. Predicting residue solvent accessibility from protein sequence by considering the sequence environment. Protein Eng 2000;13:607-609.
-
(2000)
Protein Eng
, vol.13
, pp. 607-609
-
-
Carugo, O.1
-
13
-
-
1442310611
-
Improvement in prediction of solvent accessibility by probability profiles
-
Gianese G, Bossa F, Pascarella S. Improvement in prediction of solvent accessibility by probability profiles. Protein Eng 2003;16:987-992.
-
(2003)
Protein Eng
, vol.16
, pp. 987-992
-
-
Gianese, G.1
Bossa, F.2
Pascarella, S.3
-
14
-
-
6344258643
-
Prediction of protein accessible surface areas by support vector regression
-
Yuan Z, Huang B. Prediction of protein accessible surface areas by support vector regression. Proteins 2004;57:558-564.
-
(2004)
Proteins
, vol.57
, pp. 558-564
-
-
Yuan, Z.1
Huang, B.2
-
15
-
-
33646036734
-
Two-stage support vector regression approach for predicting accessible surface areas of amino acids
-
Nguyen MN, Rajapakse JC. Two-stage support vector regression approach for predicting accessible surface areas of amino acids. Proteins 2006;63:542-550.
-
(2006)
Proteins
, vol.63
, pp. 542-550
-
-
Nguyen, M.N.1
Rajapakse, J.C.2
-
16
-
-
33646864744
-
QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization
-
Xu Z, Zhang C, Liu S, Zhou Y. QBES: predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization. Proteins 2006;63:961-966.
-
(2006)
Proteins
, vol.63
, pp. 961-966
-
-
Xu, Z.1
Zhang, C.2
Liu, S.3
Zhou, Y.4
-
17
-
-
33646596891
-
Predicting the solvent accessibility of transmembrane residues from protein sequence
-
Yuan Z, Zhang F, Davis MJ, Boden M, Teasdale RD. Predicting the solvent accessibility of transmembrane residues from protein sequence. J Proteome Res 2006;5:1063-1070.
-
(2006)
J Proteome Res
, vol.5
, pp. 1063-1070
-
-
Yuan, Z.1
Zhang, F.2
Davis, M.J.3
Boden, M.4
Teasdale, R.D.5
-
18
-
-
0037340834
-
Real value prediction of solvent accessibility from amino acid sequence
-
Ahmad S, Gromiha MM, Sarai A. Real value prediction of solvent accessibility from amino acid sequence. Proteins 2003;50:629-635.
-
(2003)
Proteins
, vol.50
, pp. 629-635
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
19
-
-
14644440766
-
Prediction of protein relative solvent accessibility with a two-stage SVM approach
-
Nguyen MN, Rajapakse JC. Prediction of protein relative solvent accessibility with a two-stage SVM approach. Proteins 2005;59:30-37.
-
(2005)
Proteins
, vol.59
, pp. 30-37
-
-
Nguyen, M.N.1
Rajapakse, J.C.2
-
20
-
-
27544475311
-
Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression
-
Wang JY, Lee HM, Ahmad S. Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression. Proteins 2005;61:481-491.
-
(2005)
Proteins
, vol.61
, pp. 481-491
-
-
Wang, J.Y.1
Lee, H.M.2
Ahmad, S.3
-
21
-
-
84899013173
-
Support vector regression machines
-
Jordan MI, Petsche T, editors. Advances in Neural Information Processing Systems. Cambridge, MA: MIT Press;
-
Drucker H, Burges CJC, Kaufman L, Smola A, Vapnik V. Support vector regression machines. In: Mozer MC, Jordan MI, Petsche T, editors. Advances in Neural Information Processing Systems. Cambridge, MA: MIT Press; 1997. pp 155-161.
-
(1997)
Mozer MC
, pp. 155-161
-
-
Drucker, H.1
Burges, C.J.C.2
Kaufman, L.3
Smola, A.4
Vapnik, V.5
-
22
-
-
0037250308
-
PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003
-
Noguchi T, Akiyama Y. PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res 2003;31:492-493.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 492-493
-
-
Noguchi, T.1
Akiyama, Y.2
-
23
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 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
Bourne, P.E.8
-
24
-
-
20844443134
-
Three-dimensional computation of atom depth in complex molecular structures
-
Varrazzo D, Bernini A, Spiga O, Ciutti A, Chiellini S, Venditti V, Bracci L, Niccolai N. Three-dimensional computation of atom depth in complex molecular structures. Bioinformatics 2005;21: 2856-2860.
-
(2005)
Bioinformatics
, vol.21
, pp. 2856-2860
-
-
Varrazzo, D.1
Bernini, A.2
Spiga, O.3
Ciutti, A.4
Chiellini, S.5
Venditti, V.6
Bracci, L.7
Niccolai, N.8
-
26
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
Sanner MF, Olson AJ, Spehner JC. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996;38:305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
27
-
-
14644400399
-
An amino acid has two sides: A new 2D measure provides a different view of solvent exposure
-
Hamelryck T. An amino acid has two sides: a new 2D measure provides a different view of solvent exposure. Proteins 2005;59:38-48.
-
(2005)
Proteins
, vol.59
, pp. 38-48
-
-
Hamelryck, T.1
-
28
-
-
0023803244
-
Predicting the secondary structure of globular proteins using neural network models
-
Qian N, Sejnowski TJ. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 1988;202:865-884.
-
(1988)
J Mol Biol
, vol.202
, pp. 865-884
-
-
Qian, N.1
Sejnowski, T.J.2
-
29
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
30
-
-
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
-
31
-
-
13944277320
-
Prediction of protein B-factor profiles
-
Yuan Z, Bailey TL, Teasdale RD. Prediction of protein B-factor profiles. Proteins 2005;58:905-912.
-
(2005)
Proteins
, vol.58
, pp. 905-912
-
-
Yuan, Z.1
Bailey, T.L.2
Teasdale, R.D.3
-
32
-
-
0032979568
-
Importance of long-range interactions in protein folding
-
Gromiha MM, Selvaraj S. Importance of long-range interactions in protein folding. Biophys Chem 1999;77:49-68.
-
(1999)
Biophys Chem
, vol.77
, pp. 49-68
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
33
-
-
1842464687
-
Inter-residue interactions in protein folding and stability
-
Gromiha MM, Selvaraj S. Inter-residue interactions in protein folding and stability. Prog Biophys Mol Biol 2004;86:235-277.
-
(2004)
Prog Biophys Mol Biol
, vol.86
, pp. 235-277
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
34
-
-
27644490770
-
Better prediction of protein contact number using a support vector regression analysis of amino acid sequence
-
Yuan Z. Better prediction of protein contact number using a support vector regression analysis of amino acid sequence. BMC Bioinformatics 2005;6:248.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 248
-
-
Yuan, Z.1
-
35
-
-
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. In: Schölkopf B, Burges C, Smola A, editors. Advances in Kernel Methods - Support Vector Learning. Cambridge, MA: MIT Press; 1999. pp 169-184.
-
(1999)
Advances in Kernel Methods - Support Vector Learning
, pp. 169-184
-
-
Joachims, T.1
-
36
-
-
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
-
37
-
-
0036700020
-
Quantifying the accessible surface area of protein residues in their local environment
-
Samanta U, Bahadur RP, Chakrabarti P. Quantifying the accessible surface area of protein residues in their local environment. Protein Eng 2002;15:659-667.
-
(2002)
Protein Eng
, vol.15
, pp. 659-667
-
-
Samanta, U.1
Bahadur, R.P.2
Chakrabarti, P.3
-
38
-
-
24644448786
-
The "first in-last out" hypothesis on protein folding revisited
-
Pintar A, Pongor S. The "first in-last out" hypothesis on protein folding revisited. Proteins 2005;60:584-590.
-
(2005)
Proteins
, vol.60
, pp. 584-590
-
-
Pintar, A.1
Pongor, S.2
|