-
1
-
-
0017187836
-
The nature of the accessible and buried surfaces in proteins
-
Chothia C (1976) The nature of the accessible and buried surfaces in proteins. J Mol Biol : 1-14.
-
(1976)
J Mol Biol
, pp. 1-14
-
-
Chothia, C.1
-
2
-
-
0022412192
-
Hydrophobicity of amino acid residues in globular proteins
-
Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH (1985) Hydrophobicity of amino acid residues in globular proteins. Science 229: 834-838.
-
(1985)
Science
, vol.229
, pp. 834-838
-
-
Rose, G.D.1
Geselowitz, A.R.2
Lesser, G.J.3
Lee, R.H.4
Zehfus, M.H.5
-
4
-
-
1342310510
-
Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins
-
Moelbert S, Emberly E, Tang C (2004) Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins. Prot Sci : 752-762.
-
(2004)
Prot Sci
, pp. 752-762
-
-
Moelbert, S.1
Emberly, E.2
Tang, C.3
-
5
-
-
66149109184
-
Solvent accessible surface area of amino acid residues in globular proteins: Correlations of apparent transfer free engergies with experimental hydrophobicity scales
-
Shaytan AK, Shaitan KV, Khokhlov AR (2009) Solvent accessible surface area of amino acid residues in globular proteins: Correlations of apparent transfer free engergies with experimental hydrophobicity scales. Biomacromolecules 10: 1224-1237.
-
(2009)
Biomacromolecules
, vol.10
, pp. 1224-1237
-
-
Shaytan, A.K.1
Shaitan, K.V.2
Khokhlov, A.R.3
-
6
-
-
0031805465
-
Assessing the impact of secondary structure and solvent accessibility on protein evolution
-
Goldman N, Thorne JL, Jones DT (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445-458.
-
(1998)
Genetics
, vol.149
, pp. 445-458
-
-
Goldman, N.1
Thorne, J.L.2
Jones, D.T.3
-
7
-
-
33748143748
-
Structural determinants of the rate of protein evolution in yeast
-
Bloom JD, Drummond DA, Arnold FH, Wilke CO (2006) Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 23: 1751-1761.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1751-1761
-
-
Bloom, J.D.1
Drummond, D.A.2
Arnold, F.H.3
Wilke, C.O.4
-
8
-
-
70349911882
-
Structural determinants of protein evolution are context-sensitive at the residue level
-
Franzosa EA, Xia Y (2009) Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol 26: 2387-2395.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2387-2395
-
-
Franzosa, E.A.1
Xia, Y.2
-
9
-
-
67649356943
-
Translationally optimal codons associate with structurally sensitive sites in proteins
-
Zhou T, Weems M, Wilke CO (2009) Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol 26: 1571-1580.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1571-1580
-
-
Zhou, T.1
Weems, M.2
Wilke, C.O.3
-
10
-
-
84867090988
-
Independent effects of protein core size and expression on structure-evolution relationships at the residue level
-
Franzosa EA, Xia Y (2012) Independent effects of protein core size and expression on structure-evolution relationships at the residue level. PLoS One 7: e46602.
-
(2012)
PLoS One
, vol.7
-
-
Franzosa, E.A.1
Xia, Y.2
-
11
-
-
84866021249
-
Modeling coding-sequence evolution within the context of residue solvent accessibility
-
Scherrer MP, Meyer AG, Wilke CO (2012) Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol Biol 12: 179.
-
(2012)
BMC Evol Biol
, vol.12
, pp. 179
-
-
Scherrer, M.P.1
Meyer, A.G.2
Wilke, C.O.3
-
12
-
-
84873445018
-
Integrating sequence variation and protein structure to identify sites under selection
-
Meyer AG, Wilke CO (2012) Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol.
-
(2012)
Mol Biol Evol
-
-
Meyer, A.G.1
Wilke, C.O.2
-
13
-
-
65349140199
-
Solvent exposure imparts similar selective pressures across a range of yeast proteins
-
Contant GC, Stadler PF (2009) Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol 26: 1155-1161.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1155-1161
-
-
Contant, G.C.1
Stadler, P.F.2
-
14
-
-
0028109886
-
Conservation and prediction of solvent accessibility in protein families
-
Rost B, Sander C (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20: 216-226.
-
(1994)
Proteins
, vol.20
, pp. 216-226
-
-
Rost, B.1
Sander, C.2
-
15
-
-
0036568293
-
Prediction of coordination number and relative solvent accessibility in proteins
-
Pollastri G, Baldi P, Fariselli P, Casadio R (2002) Prediction of coordination number and relative solvent accessibility in proteins. Proteins 47: 142-153.
-
(2002)
Proteins
, vol.47
, pp. 142-153
-
-
Pollastri, G.1
Baldi, P.2
Fariselli, P.3
Casadio, R.4
-
16
-
-
1042268067
-
Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor
-
Kim H, Park H (2004) Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor. Proteins 54: 557-562.
-
(2004)
Proteins
, vol.54
, pp. 557-562
-
-
Kim, H.1
Park, H.2
-
17
-
-
4043052866
-
Accurate prediction of solvent accessibility using neural networks-based regression
-
Adamczak R, Porollo A, Meller J (2004) Accurate prediction of solvent accessibility using neural networks-based regression. Proteins: Structure, Function, and Bioinformatics 56: 753-767.
-
(2004)
Proteins: Structure, Function, and Bioinformatics
, vol.56
, pp. 753-767
-
-
Adamczak, R.1
Porollo, A.2
Meller, J.3
-
18
-
-
14644440766
-
Prediction of protein relative solvent accessibility with a two-stage SVM approach
-
Nguyen MN, Rajapakse JC (2005) Prediction of protein relative solvent accessibility with a two-stage SVM approach. Proteins 59: 30-37.
-
(2005)
Proteins
, vol.59
, pp. 30-37
-
-
Nguyen, M.N.1
Rajapakse, J.C.2
-
19
-
-
68949213019
-
A generic method for assignment of reliability scores applied to solvent accessibility predictions
-
Petersen B, Nordahl Petersen T, Andersen P, Nielsen M, Lundegaard C (2009) A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol 9: 51.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 51
-
-
Petersen, B.1
Nordahl Petersen, T.2
Andersen, P.3
Nielsen, M.4
Lundegaard, C.5
-
20
-
-
66149176906
-
Context dependent reference states of solvent accessibility derived from native protein sturctures and assessed by predictability analysis
-
Singh H, Ahmad S (2009) Context dependent reference states of solvent accessibility derived from native protein sturctures and assessed by predictability analysis. BMC Struct Biol 9: 25.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 25
-
-
Singh, H.1
Ahmad, S.2
-
21
-
-
77957921373
-
A simple definition of structural regions in proteins and its use in analyzing interface evolution
-
Levy ED (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 403: 660-670.
-
(2010)
J Mol Biol
, vol.403
, pp. 660-670
-
-
Levy, E.D.1
-
22
-
-
33745101459
-
DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks
-
Cheng J, Sweredoski MJ, Baldi P (2006) DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Mining and Knowledge Discovery 13: 1-10.
-
(2006)
Data Mining and Knowledge Discovery
, vol.13
, pp. 1-10
-
-
Cheng, J.1
Sweredoski, M.J.2
Baldi, P.3
-
23
-
-
20144377620
-
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
-
Chen H, Zhou HX (2005) Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucl Acids Res 33: 3193-3199.
-
(2005)
Nucl Acids Res
, vol.33
, pp. 3193-3199
-
-
Chen, H.1
Zhou, H.X.2
-
24
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang G, Dunbrack RL (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
27
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
-
(1982)
J Mol Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
28
-
-
0000484499
-
Hydrophobic parameters of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides
-
Fauchere JL, Pliska VE (1983) Hydrophobic parameters of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur J Med Chem 18: 369-375.
-
(1983)
Eur J Med Chem
, vol.18
, pp. 369-375
-
-
Fauchere, J.L.1
Pliska, V.E.2
-
29
-
-
33845280446
-
Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
-
Radzicka A, Wolfenden R (1988) Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochem 27: 1664-1670.
-
(1988)
Biochem
, vol.27
, pp. 1664-1670
-
-
Radzicka, A.1
Wolfenden, R.2
-
30
-
-
34247626293
-
Partitioning of amino acid side chains into lipid bilayers: Results from computer simulations and comparison to experiment
-
MacCallum JL, Bennett WFD, Tieleman DP (2007) Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J Gen Physiol 129: 371-377.
-
(2007)
J Gen Physiol
, vol.129
, pp. 371-377
-
-
MacCallum, J.L.1
Bennett, W.F.D.2
Tieleman, D.P.3
-
31
-
-
79959928058
-
Side chain hydrophobicity scales derived from transmembrane protein folding into lipid bilayers
-
Moon CP, Fleming KG (2011) Side chain hydrophobicity scales derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci USA 108: 10174-10177.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 10174-10177
-
-
Moon, C.P.1
Fleming, K.G.2
-
32
-
-
0030005250
-
Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
-
Wimley WC, Creamer TP, White SH (1996) Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochem 35: 5109-5124.
-
(1996)
Biochem
, vol.35
, pp. 5109-5124
-
-
Wimley, W.C.1
Creamer, T.P.2
White, S.H.3
-
33
-
-
0037340834
-
Real-value prediction of solvent accessibility from amino acid sequence
-
Ahmad S, Gromiha MM, Sarai A (2003) Real-value prediction of solvent accessibility from amino acid sequence. Proteins 50: 629-635.
-
(2003)
Proteins
, vol.50
, pp. 629-635
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
34
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
35
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55: 379-400.
-
(1971)
J Mol Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
37
-
-
0029922443
-
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
-
Tomii K, Kanehisa M (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 9: 27-36.
-
(1996)
Protein Eng
, vol.9
, pp. 27-36
-
-
Tomii, K.1
Kanehisa, M.2
-
38
-
-
38549155006
-
AAindex: Amino acid index database, progress report 2008
-
Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, et al. (2008) AAindex: amino acid index database, progress report 2008. Nucleic Acids Res 36: D202-D205.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kawashima, S.1
Pokarowski, P.2
Pokarowska, M.3
Kolinski, A.4
Katayama, T.5
-
39
-
-
0000243829
-
PROCHECK - A program to check the stereochemical quality of protein structures
-
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J App Cryst 26: 283-291.
-
(1993)
J App Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
40
-
-
84885098469
-
PeptideBuilder: A simple Python library to generate model peptides
-
Tien MZ, Sydykova DK, Meyer AG, Wilke CO (2013) PeptideBuilder: a simple Python library to generate model peptides. PeerJ 1: e80.
-
(2013)
PeerJ
, vol.1
-
-
Tien, M.Z.1
Sydykova, D.K.2
Meyer, A.G.3
Wilke, C.O.4
|