-
1
-
-
0042386609
-
The relationship between sequence and interaction divergence in proteins
-
Aloy P, Ceulemans H, Stark A, Russell RB. 2003. The relationship between sequence and interaction divergence in proteins. J Mol Biol. 332:989-998.
-
(2003)
J Mol Biol
, vol.332
, pp. 989-998
-
-
Aloy, P.1
Ceulemans, H.2
Stark, A.3
Russell, R.B.4
-
2
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res. 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
-
3
-
-
0642340510
-
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps
-
Berrera M, Molinari H, Fogolari F. 2003. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics. 4:8.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 8
-
-
Berrera, M.1
Molinari, H.2
Fogolari, F.3
-
4
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES. 2004. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci. 13:190-202.
-
(2004)
Protein Sci
, vol.13
, pp. 190-202
-
-
Caffrey, D.R.1
Somaroo, S.2
Hughes, J.D.3
Mintseris, J.4
Huang, E.S.5
-
5
-
-
33846811404
-
-
Felsenstein J. 1993. PHYLIP (phylogeny inference package, Version 3.5c. Distributed by the author. Seattle WA, Department of Genetics, University of Washington
-
Felsenstein J. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author. Seattle (WA): Department of Genetics, University of Washington.
-
-
-
-
6
-
-
0036184351
-
Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations
-
Fornasari MS, Parisi G, Echave J. 2002. Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations. Mol Biol Evol. 19:352-356.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 352-356
-
-
Fornasari, M.S.1
Parisi, G.2
Echave, J.3
-
7
-
-
0027423317
-
Simple diagnostic statistical tests of models for DNA substitution
-
Goldman N. 1993. Simple diagnostic statistical tests of models for DNA substitution. J Mol Evol. 37:650-661.
-
(1993)
J Mol Evol
, vol.37
, pp. 650-661
-
-
Goldman, N.1
-
8
-
-
2942553723
-
Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking
-
Halperin I, Wolfson, Nussinov R. 2004. Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure. 12:1027-1038.
-
(2004)
Structure
, vol.12
, pp. 1027-1038
-
-
Halperin, I.1
-
9
-
-
0022376704
-
Dating of the human-ape splitting by molecular clock of mitochondrial DNA
-
Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by molecular clock of mitochondrial DNA. J Mol Biol. 22:160-174.
-
(1985)
J Mol Biol
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
10
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
-
(1992)
Comput Appl Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
11
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM. 1996. Principles of protein-protein interactions. Proc Natl Acad Sci USA. 93:13-20.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
12
-
-
0028224689
-
Modeling compact denatured states of proteins
-
Lattman EE, Fiebig KM, Dill KA. 1994. Modeling compact denatured states of proteins. Biochemistry. 33:6158-6166.
-
(1994)
Biochemistry
, vol.33
, pp. 6158-6166
-
-
Lattman, E.E.1
Fiebig, K.M.2
Dill, K.A.3
-
13
-
-
7944225979
-
Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking
-
Li X, Keskin O, Ma B, Nussinov R, Liang J. 2004. Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol. 344:781-795.
-
(2004)
J Mol Biol
, vol.344
, pp. 781-795
-
-
Li, X.1
Keskin, O.2
Ma, B.3
Nussinov, R.4
Liang, J.5
-
14
-
-
0025908265
-
The role of internal packing interactions in determining the structure and stability of a protein
-
Lim WA, Sauer RT. 1991. The role of internal packing interactions in determining the structure and stability of a protein. J Mol Biol. 219:359-376.
-
(1991)
J Mol Biol
, vol.219
, pp. 359-376
-
-
Lim, W.A.1
Sauer, R.T.2
-
15
-
-
23344451687
-
Structure, function, and evolution of transient and obligate protein-protein interactions
-
Mintseris J, Weng Z. 2005. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA. 102:10930-10935.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10930-10935
-
-
Mintseris, J.1
Weng, Z.2
-
16
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247:536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
17
-
-
0041312697
-
Diversity of protein-protein interactions
-
Nooren IM, Thornton JM. 2003. Diversity of protein-protein interactions. EMBO J. 22:3486-3492.
-
(2003)
EMBO J
, vol.22
, pp. 3486-3492
-
-
Nooren, I.M.1
Thornton, J.M.2
-
18
-
-
0037229456
-
Analysing six types of protein-protein interfaces
-
Ofran Y, Rost B. 2003. Analysing six types of protein-protein interfaces. J Mol Biol. 325:377-387.
-
(2003)
J Mol Biol
, vol.325
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
19
-
-
0026474167
-
Structural constraints on residue substitution
-
Overington J. 1992. Structural constraints on residue substitution. Genet Eng. 14:231-249.
-
(1992)
Genet Eng
, vol.14
, pp. 231-249
-
-
Overington, J.1
-
20
-
-
0025104478
-
Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
-
Overington J, Johnson MS, Sali A, Blundell TL. 1990. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci. 241:132-145.
-
(1990)
Proc Biol Sci
, vol.241
, pp. 132-145
-
-
Overington, J.1
Johnson, M.S.2
Sali, A.3
Blundell, T.L.4
-
21
-
-
0035028705
-
Structural constraints and emergence of sequence patterns in protein evolution
-
Parisi G, Echave J. 2001. Structural constraints and emergence of sequence patterns in protein evolution. Mol Biol Evol. 18:750-756.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 750-756
-
-
Parisi, G.1
Echave, J.2
-
22
-
-
33845548778
-
The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily
-
Parisi G, Echave J. 2004. The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily. BMC Evol Biol. 4:41.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 41
-
-
Parisi, G.1
Echave, J.2
-
23
-
-
13444305208
-
Generality of the structurally constrained protein evolution model: Assessment on representatives of the four main fold classes
-
Parisi G, Echave J. 2005. Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes. Gene. 345:45-53.
-
(2005)
Gene
, vol.345
, pp. 45-53
-
-
Parisi, G.1
Echave, J.2
-
24
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
Pollock DD, Taylor WR. 1997. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10:647-657.
-
(1997)
Protein Eng
, vol.10
, pp. 647-657
-
-
Pollock, D.D.1
Taylor, W.R.2
-
25
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 21:676-679.
-
(2005)
Bioinformatics
, vol.21
, pp. 676-679
-
-
Pond, S.L.1
Frost, S.D.2
Muse, S.V.3
-
26
-
-
0028081403
-
Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility
-
Russell RB, Barton GJ. 1994. Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. J Mol Biol. 244:332-350.
-
(1994)
J Mol Biol
, vol.244
, pp. 332-350
-
-
Russell, R.B.1
Barton, G.J.2
-
27
-
-
0028051828
-
Derivation of rules for comparative protein modeling from a protein structure alignments
-
Sali A, Overington JP. 1994. Derivation of rules for comparative protein modeling from a protein structure alignments. Protein Sci. 3:1582-1596.
-
(1994)
Protein Sci
, vol.3
, pp. 1582-1596
-
-
Sali, A.1
Overington, J.P.2
-
28
-
-
0034332976
-
Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score
-
Vendruscolo M, Mirny LA, Shakhnovich EI, Domany E. 2000. Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score. Proteins. 41:192-201.
-
(2000)
Proteins
, vol.41
, pp. 192-201
-
-
Vendruscolo, M.1
Mirny, L.A.2
Shakhnovich, E.I.3
Domany, E.4
-
29
-
-
0031893269
-
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
-
Xu J, Baase WA, Baldwin E, Matthews BW. 1998. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci. 7:158-177.
-
(1998)
Protein Sci
, vol.7
, pp. 158-177
-
-
Xu, J.1
Baase, W.A.2
Baldwin, E.3
Matthews, B.W.4
|