-
1
-
-
0029738719
-
Characterizations of diverse residue clusters in protein three-dimensional structures
-
Karlin S., Zhu Z. Characterizations of diverse residue clusters in protein three-dimensional structures. Proc. Natl Acad. Sci. USA. 93:1996;8344-8349.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 8344-8349
-
-
Karlin, S.1
Zhu, Z.2
-
2
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf R., Xenarios I., Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol. 307:2001;1487-1502.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
3
-
-
0035838976
-
Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
-
Aloy P., Querol E., Aviles F., Sternberg M. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311:2001;395-408.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 395-408
-
-
Aloy, P.1
Querol, E.2
Aviles, F.3
Sternberg, M.4
-
4
-
-
0036300444
-
Structural clusters of evolutionary trace residues are statistically significant and common in proteins
-
Madabushi S., Yao H., Marsh M., Kristensen D., Philippi A., Sowa M., Lichtarge O. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J. Mol. Biol. 316:2002;139-154.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 139-154
-
-
Madabushi, S.1
Yao, H.2
Marsh, M.3
Kristensen, D.4
Philippi, A.5
Sowa, M.6
Lichtarge, O.7
-
5
-
-
85031148435
-
An accurate, sensitive, and scalable method to identify functional sites in protein structures
-
In the Press
-
Yao, H., Kristensen, D., Mihalek, I., Sowa, M., Shaw, C., Kavraki, L., Kimmel, M. & Lichtarge, O. (2002). An accurate, sensitive, and scalable method to identify functional sites in protein structures. J. Mol. Biol. In the Press.
-
(2002)
J. Mol. Biol.
-
-
Yao, H.1
Kristensen, D.2
Mihalek, I.3
Sowa, M.4
Shaw, C.5
Kavraki, L.6
Kimmel, M.7
Lichtarge, O.8
-
6
-
-
0038009021
-
Supplement: Fourth meeting on the critical assessment of techniques for protein structure prediction
-
Various authors (2001). Supplement: fourth meeting on the critical assessment of techniques for protein structure prediction. Proteins: Struct. Funct. Genet. 45.
-
(2001)
Proteins: Struct. Funct. Genet.
, vol.45
-
-
-
8
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T., Karplus M. Effective energy functions for protein structure prediction. Curr. Opin. Struct. Biol. 10:2000;139-145.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 139-145
-
-
Lazaridis, T.1
Karplus, M.2
-
10
-
-
0036535895
-
Protein folding: The free energy surface
-
Gruebele M. Protein folding: the free energy surface. Curr. Opin. Struct. Biol. 12:2002;161-168.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 161-168
-
-
Gruebele, M.1
-
12
-
-
0036667733
-
Knowledge-based potential functions in protein design
-
Russ W., Ranganathan R. Knowledge-based potential functions in protein design. Curr. Opin. Struct. Biol. 12:2002;447-452.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 447-452
-
-
Russ, W.1
Ranganathan, R.2
-
13
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T., Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288:1999;477-487.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
14
-
-
0031557390
-
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
-
Park B., Huang E., Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 266:1997;831-846.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 831-846
-
-
Park, B.1
Huang, E.2
Levitt, M.3
-
15
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
Simons K., Ruczinski I., Kooperberg C., Fox B., Bystroff C., Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins: Struct. Funct. Genet. 34:1999;82-95.
-
(1999)
Proteins: Struct. Funct. Genet.
, vol.34
, pp. 82-95
-
-
Simons, K.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.4
Bystroff, C.5
Baker, D.6
-
16
-
-
0035314042
-
Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
-
Bonneau R., Strauss C., Baker D. Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins: Struct. Funct. Genet. 43:2001;1-11.
-
(2001)
Proteins: Struct. Funct. Genet.
, vol.43
, pp. 1-11
-
-
Bonneau, R.1
Strauss, C.2
Baker, D.3
-
17
-
-
0029101826
-
Recognizing native folds by the arrangement of hydrophobic and polar residues
-
Huang E., Subbiah S., Levitt M. Recognizing native folds by the arrangement of hydrophobic and polar residues. J. Mol. Biol. 252:1995;709-720.
-
(1995)
J. Mol. Biol.
, vol.252
, pp. 709-720
-
-
Huang, E.1
Subbiah, S.2
Levitt, M.3
-
18
-
-
0029871791
-
Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations
-
Huang E., Subbiah S., Tsai J., Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J. Mol. Biol. 257:1996;716-725.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 716-725
-
-
Huang, E.1
Subbiah, S.2
Tsai, J.3
Levitt, M.4
-
19
-
-
0036073603
-
Contact order and ab initio protein structure prediction
-
Bonneau R., Ruczinski I., Tsai J., Baker D. Contact order and ab initio protein structure prediction. Proteins Sci. 11:2002;1937-1944.
-
(2002)
Proteins Sci.
, vol.11
, pp. 1937-1944
-
-
Bonneau, R.1
Ruczinski, I.2
Tsai, J.3
Baker, D.4
-
20
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco K., Simons K., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:1998;985-994.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 985-994
-
-
Plaxco, K.1
Simons, K.2
Baker, D.3
-
21
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos F., Helmer-Citterich M., Ausiello G., Valencia A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271:1997;511-523.
-
(1997)
J. Mol. Biol.
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
Valencia, A.4
-
23
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
Olmea O., Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold. Des. 2:1997;S25-S32.
-
(1997)
Fold. Des.
, vol.2
-
-
Olmea, O.1
Valencia, A.2
-
25
-
-
0027764344
-
Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
-
Livingstone C., Barton G. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci. 9:1993;745-775.
-
(1993)
Comput. Appl. Biosci.
, vol.9
, pp. 745-775
-
-
Livingstone, C.1
Barton, G.2
-
26
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O., Bourne H., Cohen F. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257:1996;342-358.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.2
Cohen, F.3
-
27
-
-
0035254936
-
Conserved key amino acid positions (CKAAP's) derived from the analysis of common substructures in proteins
-
Reddy, B., Li, W., Shindyalov, I. & Bourne, P. (2001). Conserved key amino acid positions (CKAAP's) derived from the analysis of common substructures in proteins. Proteins: Struct. Funct. Genet. 42, 148-163.
-
(2001)
Proteins: Struct. Funct. Genet.
, vol.42
, pp. 148-163
-
-
Reddy, B.1
Li, W.2
Shindyalov, I.3
Bourne, P.4
-
28
-
-
0036145469
-
Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function
-
Friedberg I., Margalit H. Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. Proteins Sci. 11:2002;350-360.
-
(2002)
Proteins Sci.
, vol.11
, pp. 350-360
-
-
Friedberg, I.1
Margalit, H.2
-
29
-
-
0033550256
-
Effective use of sequence correlation and conservation in fold recognition
-
Olmea O., Rost B., Valencia A. Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol. 295:1999;1221-1239.
-
(1999)
J. Mol. Biol.
, vol.295
, pp. 1221-1239
-
-
Olmea, O.1
Rost, B.2
Valencia, A.3
-
30
-
-
0029664921
-
Evolutionarily conserved galphabetagamma binding surfaces support a model of the g protein-receptor complex
-
Lichtarge O., Bourne H., Cohen F. Evolutionarily conserved galphabetagamma binding surfaces support a model of the g protein-receptor complex. Proc. Natl Acad. Sci. USA. 93:1996;1483-1488.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 1483-1488
-
-
Lichtarge, O.1
Bourne, H.2
Cohen, F.3
-
31
-
-
0034652331
-
A regulator of g protein signaling interaction surface linked to effector specificity
-
Sowa M.E., He T., Wensel T.G., Lichtarge O. A regulator of g protein signaling interaction surface linked to effector specificity. Proc. Natl Acad. Sci. USA. 97:2000;1483-1488.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 1483-1488
-
-
Sowa, M.E.1
He, T.2
Wensel, T.G.3
Lichtarge, O.4
-
32
-
-
0030614427
-
Receptor and betagamma binding sites in the alpha subunit of the retinal g protein transducin
-
Onrust R.P., Herzmark P.C., Garcia P.D., Lichtarge O., Kingsley C., Bourne H.R. Receptor and betagamma binding sites in the alpha subunit of the retinal g protein transducin. Science. 275:1997;381-384.
-
(1997)
Science
, vol.275
, pp. 381-384
-
-
Onrust, R.P.1
Herzmark, P.C.2
Garcia, P.D.3
Lichtarge, O.4
Kingsley, C.5
Bourne, H.R.6
-
33
-
-
0029785147
-
Mapping the protein universe
-
Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-602.
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
34
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O., Sowa M. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12:2002;21-27.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 21-27
-
-
Lichtarge, O.1
Sowa, M.2
-
35
-
-
0033954256
-
The Protein Data Bank
-
Berman H., Westbrook J., Feng Z., Gilliland G., Bhat T., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.5
Weissig, H.6
-
36
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd A., Orengo C., Thornton M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1113-1143
-
-
Todd, A.1
Orengo, C.2
Thornton, M.3
-
37
-
-
0030801002
-
Gapped blast and psi-blast: A new generation of protein database search programs
-
Altschul S., Madden T., Schaffer A., Zhang J., Zhang Z., Miller W., Lipman D. Gapped blast and psi-blast: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
39
-
-
0027968068
-
ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson J., Higgins D., Gibson T. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.1
Higgins, D.2
Gibson, T.3
-
40
-
-
0029987862
-
Energy functions that discriminate x-ray and near-native folds from well-constructed decoys
-
Park B., Levitt M. Energy functions that discriminate x-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258:1996;367-392.
-
(1996)
J. Mol. Biol.
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
41
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons K., Kooperberg C., Huang E., Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268:1997;209-225.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 209-225
-
-
Simons, K.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
43
-
-
0034733381
-
Ab initio construction of protein tertiary structures using a hierarchical approach
-
Xia Y., Huang E., Levitt M. Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol. 300:2000;171-185.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 171-185
-
-
Xia, Y.1
Huang, E.2
Levitt, M.3
|