-
1
-
-
0028180367
-
Bona fide prediction of aspects of protein conformation. Assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences
-
Benner,S.A., Badcoe,I., Cohen,M.A. and Gerloff,D.L. (1994) Bona fide prediction of aspects of protein conformation. Assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences. J. Mol. Biol., 235, 926-958.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 926-958
-
-
Benner, S.A.1
Badcoe, I.2
Cohen, M.A.3
Gerloff, D.L.4
-
2
-
-
0029889222
-
Identification of functional residues and secondary structure from protein multiple sequence alignment
-
Livingstone,C.D. and Barton,G.J. (1996) Identification of functional residues and secondary structure from protein multiple sequence alignment. Meth. Enzymol., 266, 497-512.
-
(1996)
Meth. Enzymol.
, vol.266
, pp. 497-512
-
-
Livingstone, C.D.1
Barton, G.J.2
-
3
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge,O., Bourne,H.R. and Cohen,F.E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
4
-
-
0025935158
-
Patterns of divergence in homologous proteins as indicators of secondary and tertiary structures: The catalytic domain of protein kinases
-
Benner,S.A. and Gerloff,D. (1991) Patterns of divergence in homologous proteins as indicators of secondary and tertiary structures: the catalytic domain of protein kinases. Advan. Enzyme Regulat., 31, 121-181.
-
(1991)
Advan. Enzyme Regulat.
, vol.31
, pp. 121-181
-
-
Benner, S.A.1
Gerloff, D.2
-
5
-
-
0025912824
-
Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics
-
Kimura,M. (1991) Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics. Proc. Natl Acad. Sci. USA, 88, 5969-5973.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 5969-5973
-
-
Kimura, M.1
-
6
-
-
0034614321
-
Do proteins learn to evolve? The Hopfield network as a basis for the understanding of protein evolution
-
Pritchard,L. and Dufton,M.J. (2000) Do proteins learn to evolve? The Hopfield network as a basis for the understanding of protein evolution. J. Theor. Biol., 202, 77-86.
-
(2000)
J. Theor. Biol.
, vol.202
, pp. 77-86
-
-
Pritchard, L.1
Dufton, M.J.2
-
7
-
-
0037069428
-
Dobzhansky-Muller incompatibilities in protein evolution
-
Kondrashov,A.S., Sunyaev,S. and Kondrashov,F.A. (2002) Dobzhansky-Muller incompatibilities in protein evolution. Proc. Natl Acad. Sci. USA, 99, 14878-14883.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14878-14883
-
-
Kondrashov, A.S.1
Sunyaev, S.2
Kondrashov, F.A.3
-
8
-
-
0026560853
-
Correlation of co-ordinated amino acid changes at the two-domain interface of cysteine proteases with protein stability
-
Vernet,T., Tessier,D.C., Khouri,H.E. and Altschuh,D. (1992) Correlation of co-ordinated amino acid changes at the two-domain interface of cysteine proteases with protein stability. J. Mol. Biol., 224, 501-509.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 501-509
-
-
Vernet, T.1
Tessier, D.C.2
Khouri, H.E.3
Altschuh, D.4
-
9
-
-
0033616825
-
Mutually compensatory mutations during evolution of the tetramerization domain of tumor supressor p53 lead to impaired hetero-oligomerization
-
Mateu,M.G. and Fersht,A.R. (1999) Mutually compensatory mutations during evolution of the tetramerization domain of tumor supressor p53 lead to impaired hetero-oligomerization. Proc. Natl Acad. Sci. USA, 96, 3595-3599.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 3595-3599
-
-
Mateu, M.G.1
Fersht, A.R.2
-
10
-
-
0033538423
-
Guiding a docking mode by phage display: Selection of correlated mutations at the staphylokinase-plasmin interface
-
Jespers,L., Lijnen,H.R., Vanwetswinkel,S., Van Hoef,B., Brepoels,K., Collen,D. and De Maeyer,M. (1999) Guiding a docking mode by phage display: selection of correlated mutations at the staphylokinase-plasmin interface. J. Mol. Biol., 290, 471-479.
-
(1999)
J. Mol. Biol.
, vol.290
, pp. 471-479
-
-
Jespers, L.1
Lijnen, H.R.2
Vanwetswinkel, S.3
Van Hoef, B.4
Brepoels, K.5
Collen, D.6
De Maeyer, M.7
-
11
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Göbel,U., Sander,C., Schneider,R. and Valencia,A. (1994) Correlated mutations and residue contacts in proteins. Prot. Struct. Funct. Genet., 18, 309-317.
-
(1994)
Prot. Struct. Funct. Genet.
, vol.18
, pp. 309-317
-
-
Göbel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
12
-
-
0028084754
-
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
-
Shindyalov,I.N., Kolchanov,N.A. and Sander,C. (1994) Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Prot. Eng., 7, 349-358.
-
(1994)
Prot. Eng.
, vol.7
, pp. 349-358
-
-
Shindyalov, I.N.1
Kolchanov, N.A.2
Sander, C.3
-
13
-
-
0033536602
-
Evolutionary conserved pathways of energetic connectivity in protein families
-
Lockless,S.W. and Ranganathan,R. (1999) Evolutionary conserved pathways of energetic connectivity in protein families. Science, 286, 295-299.
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
14
-
-
0033550256
-
Effective use of sequence correlation and conservation in fold recognition
-
Olmea,O., Rost,B. and Valencia,A. (1999) Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol., 293, 1221-1239.
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 1221-1239
-
-
Olmea, O.1
Rost, B.2
Valencia, A.3
-
15
-
-
0032571390
-
Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignment
-
Ortiz,A.R., Kolinski,A. and Skolnick,J. (1998) Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignment. J. Mol. Biol., 277, 419-448.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 419-448
-
-
Ortiz, A.R.1
Kolinski, A.2
Skolnick, J.3
-
16
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos,F., Helmer-Citterich,M., Ausiello,G. and Valencia,A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271, 511-523.
-
(1997)
J. Mol. Biol.
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
Valencia, A.4
-
17
-
-
0033047710
-
A neural network based predictor of residue contacts in proteins
-
Fariselli,P. and Casadio,R. (1999) A neural network based predictor of residue contacts in proteins. Protein Eng., 12, 15-21.
-
(1999)
Protein Eng.
, vol.12
, pp. 15-21
-
-
Fariselli, P.1
Casadio, R.2
-
18
-
-
0034721944
-
Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
-
Larson,S.M., Di Nardo,A.A. and Davidson,A.R. (2000) Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol., 303, 433-446.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 433-446
-
-
Larson, S.M.1
Di Nardo, A.A.2
Davidson, A.R.3
-
19
-
-
0000304539
-
On the constancy of the hydrophobic nucleus volume in molecules of myoglobins and hemoglobins
-
Lim,V.I. and Ptitsyn,O.B. (1970) On the constancy of the hydrophobic nucleus volume in molecules of myoglobins and hemoglobins. Mol. Biol. (USSR), 4, 372-382.
-
(1970)
Mol. Biol. (USSR)
, vol.4
, pp. 372-382
-
-
Lim, V.I.1
Ptitsyn, O.B.2
-
20
-
-
0028221642
-
Volume changes in protein evolution
-
Gerstein,M., Sonnhammer,E.L. and Chothia,C. (1994) Volume changes in protein evolution. J. Mol. Biol., 236, 1076-1078.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1076-1078
-
-
Gerstein, M.1
Sonnhammer, E.L.2
Chothia, C.3
-
21
-
-
0033600935
-
Prediction of potential GPI-modification sites in proprotein sequences
-
Eisenhaber,B., Bork,P. and Eisenhaber,F. (1999) Prediction of potential GPI-modification sites in proprotein sequences. J. Mol. Biol., 292, 741-758.
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 741-758
-
-
Eisenhaber, B.1
Bork, P.2
Eisenhaber, F.3
-
22
-
-
0035182669
-
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions
-
Afonnikov,D.A., Oshchepkov,D.Y. and Kolchanov,N.A. (2001) Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics, 17, 1035-1046.
-
(2001)
Bioinformatics
, vol.17
, pp. 1035-1046
-
-
Afonnikov, D.A.1
Oshchepkov, D.Y.2
Kolchanov, N.A.3
-
23
-
-
0029922443
-
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
-
Tomii,K. and 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
-
25
-
-
0008117663
-
Correlated mutations in protein sequences: Phylogenetic and structural effects
-
Monograph Series of the Institute for Mathematical Statistics, Hayward, CA
-
Lapedes,A.S., Giraud,B.G., Liu,L.C. and Stormo,G.D. (1997) Correlated mutations in protein sequences: phylogenetic and structural effects. In Proceedings of the AMS/SIAM Conference on Statistics in Molecular Biology, Vol. 33, Monograph Series of the Institute for Mathematical Statistics, Hayward, CA, pp. 236-256.
-
(1997)
Proceedings of the AMS/SIAM Conference on Statistics in Molecular Biology
, vol.33
, pp. 236-256
-
-
Lapedes, A.S.1
Giraud, B.G.2
Liu, L.C.3
Stormo, G.D.4
-
26
-
-
0006711790
-
Stability of the partial correlation coefficient estimates for residue characteristics at different positions of amino acid sequences
-
Novosibirsk, Russia, August 7-11, 2000, Institute of Cytology and Genetics, Novosibirsk
-
Afonnikov,D.A. (2000) Stability of the partial correlation coefficient estimates for residue characteristics at different positions of amino acid sequences. The Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2000), Novosibirsk, Russia, August 7-11, 2000, Vol. 2, Institute of Cytology and Genetics, Novosibirsk, pp. 207-210.
-
(2000)
The Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2000)
, vol.2
, pp. 207-210
-
-
Afonnikov, D.A.1
-
27
-
-
0022203256
-
Phylogenies and the comparative method
-
Felsenstein,J. (1985) Phylogenies and the comparative method. Am. Nat., 125, 1-15.
-
(1985)
Am. Nat.
, vol.125
, pp. 1-15
-
-
Felsenstein, J.1
-
28
-
-
0030743758
-
Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
-
Pollock,D.D. and Taylor,W.R. (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
-
29
-
-
0024544755
-
A fast and sensitive multiple sequence alignment algorithm
-
Vingron,M. and Argos,P. (1989) A fast and sensitive multiple sequence alignment algorithm. CABIOS, 5, 115-121.
-
(1989)
CABIOS
, vol.5
, pp. 115-121
-
-
Vingron, M.1
Argos, P.2
-
30
-
-
0028043552
-
Position-based sequence weights
-
Henikoff,S. and Henikoff,J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 574-578
-
-
Henikoff, S.1
Henikoff, J.G.2
-
31
-
-
0028832687
-
Covariation of residues in homeodomain sequence family
-
Clarke,N.D. (1995) Covariation of residues in homeodomain sequence family. Prot. Sci., 4, 2269-2278.
-
(1995)
Prot. Sci.
, vol.4
, pp. 2269-2278
-
-
Clarke, N.D.1
-
32
-
-
0035465219
-
Can correlated mutations in protein domain families be used for protein design?
-
Nagl,S.B. (2001) Can correlated mutations in protein domain families be used for protein design? Brief Bioinform., 2, 279-288.
-
(2001)
Brief. Bioinform.
, vol.2
, pp. 279-288
-
-
Nagl, S.B.1
-
33
-
-
0033977832
-
Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis
-
Atchley,W.R., Wollenberg,K.R., Fitch,W.M., Terhalle,W. and Dress,A.W. (2000) Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol. Biol. Evol., 17, 164-178.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 164-178
-
-
Atchley, W.R.1
Wollenberg, K.R.2
Fitch, W.M.3
Terhalle, W.4
Dress, A.W.5
-
35
-
-
3242877696
-
Contribution of coordinated substitutions to the constancy of physicochemical properties of ATP-binding loop in protein kinases
-
Kolchanov,N. and Hofestaedt,R. eds, Kluwer Academic Publishers, Boston/Dordrecht/London
-
Afonnikov,D.A. (2004) Contribution of coordinated substitutions to the constancy of physicochemical properties of ATP-binding loop in protein kinases. In Kolchanov,N. and Hofestaedt,R. (eds), Bioinformatics of Genome Regulation and Structure. Kluwer Academic Publishers, Boston/Dordrecht/London, pp. 223-230.
-
(2004)
Bioinformatics of Genome Regulation and Structure
, pp. 223-230
-
-
Afonnikov, D.A.1
-
36
-
-
0019934717
-
The helical hydrophobic moment: A measure of the amphiphilicity of a helix
-
Eisenberg,D., Weiss,R.M. and Terwilliger,T.C. (1982) The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature, 299, 371-374.
-
(1982)
Nature
, vol.299
, pp. 371-374
-
-
Eisenberg, D.1
Weiss, R.M.2
Terwilliger, T.C.3
-
37
-
-
0006635932
-
F distribution
-
Armitage,P. and Colton,T. eds, John Wiley & Sons, Chichester
-
Selvin,S. (1998) F distribution. In Armitage,P. and Colton,T. (eds), Encyclopedia of Biostatistics. John Wiley & Sons, Chichester, vol. 2, pp. 1469-1472.
-
(1998)
Encyclopedia of Biostatistics
, vol.2
, pp. 1469-1472
-
-
Selvin, S.1
|