-
1
-
-
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.X., and Sternberg, M.J. 2001. 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: 395-408.
-
(2001)
J. Mol. Biol.
, vol.311
, pp. 395-408
-
-
Aloy, P.1
Querol, E.2
Aviles, F.X.3
Sternberg, M.J.4
-
2
-
-
8544221118
-
Network analysis of protein structures identifies functional residues
-
Amitai, G., Shemesh, A., Sitbon, E., Shklar, M., Netanely, D., Venger, I., and Pietrokovski, S. 2004. Network analysis of protein structures identifies functional residues. J. Mol. Biol. 344: 1135-1146.
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 1135-1146
-
-
Amitai, G.1
Shemesh, A.2
Sitbon, E.3
Shklar, M.4
Netanely, D.5
Venger, I.6
Pietrokovski, S.7
-
3
-
-
0346057951
-
Small-world communication of residues and significance for protein dynamics. Small-world view of the amino acids that play a key role in protein folding
-
Atilgan, A.R., Akan, P., Baysal, C., Vendruscolo, M., Dokholyan, N.V., Paci, E., and Karplus, M. 2004. Small-world communication of residues and significance for protein dynamics. Small-world view of the amino acids that play a key role in protein folding. Biophys. J. 86: 85-91.
-
(2004)
Biophys. J.
, vol.86
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
Vendruscolo, M.4
Dokholyan, N.V.5
Paci, E.6
Karplus, M.7
-
4
-
-
0035171884
-
BIND - The biomolecular interaction network database
-
Bader, G.D., Donaldson, I., Wolting, C., Ouellette, B.F., Pawson, T., and Hogue, C.W. 2001. BIND - The biomolecular interaction network database. Nucleic Acids Res. 29: 242-245.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 242-245
-
-
Bader, G.D.1
Donaldson, I.2
Wolting, C.3
Ouellette, B.F.4
Pawson, T.5
Hogue, C.W.6
-
5
-
-
0033954256
-
The protein databank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The protein databank. 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
-
6
-
-
12944331889
-
Small-world network approach to identify key residues in protein-protein interaction
-
del Sol, A. and O'Meara, P. 2004. Small-world network approach to identify key residues in protein-protein interaction. Proteins 58: 672-682.
-
(2004)
Proteins
, vol.58
, pp. 672-682
-
-
Del Sol, A.1
O'Meara, P.2
-
7
-
-
17444396776
-
Topology of small-world networks of protein-protein complex structures
-
del Sol, A., Fujihashi, H., and O'Meara, P. 2005. Topology of small-world networks of protein-protein complex structures. Bioinformatics 21: 1311-1315.
-
(2005)
Bioinformatics
, vol.21
, pp. 1311-1315
-
-
Del Sol, A.1
Fujihashi, H.2
O'Meara, P.3
-
8
-
-
33745461893
-
Residues crucial for maintaining short paths in network communication mediate signaling in proteins
-
del Sol, A., Fujihashi, H., Amoros, D., and Nussinov, R. 2006. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2: http://www.nature.com/msb/journal/v2/n1/ synopsis/msb4100063.html.
-
(2006)
Mol. Syst. Biol.
, vol.2
-
-
Del Sol, A.1
Fujihashi, H.2
Amoros, D.3
Nussinov, R.4
-
9
-
-
0037470597
-
Automatic methods for predicting functionally important residues
-
del Sol Mesa, A., Pazos, F., and Valencia, A. 2003. Automatic methods for predicting functionally important residues. J. Mol. Biol. 326: 1289-1302.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1289-1302
-
-
Del Sol Mesa, A.1
Pazos, F.2
Valencia, A.3
-
10
-
-
0037173002
-
Topological determinants of protein fold
-
Dokholyan, N.V., Li, L., Ding, F., and Shakhnovich, E.I. 2002. Topological determinants of protein fold. Proc. Natl. Acad. Sci. 99: 8637-8641.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 8637-8641
-
-
Dokholyan, N.V.1
Li, L.2
Ding, F.3
Shakhnovich, E.I.4
-
11
-
-
2542445427
-
ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E., and Ben-Tal, N. 2003. ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
-
(2003)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
Martz, E.6
Ben-Tal, N.7
-
12
-
-
30144442036
-
A method for localizing ligand binding pockets in protein structures
-
Glaser, F., Morris, R.J., Najmanovich, R.J., Laskowski, R.A., and Thornton, J.M. 2006. A method for localizing ligand binding pockets in protein structures. Proteins 62: 479-488.
-
(2006)
Proteins
, vol.62
, pp. 479-488
-
-
Glaser, F.1
Morris, R.J.2
Najmanovich, R.J.3
Laskowski, R.A.4
Thornton, J.M.5
-
13
-
-
0242720597
-
Uncovering network systems within protein structures
-
Greene, L. and Higman, V. 2003. Uncovering network systems within protein structures. J. Mol. Biol. 334: 781-791.
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 781-791
-
-
Greene, L.1
Higman, V.2
-
14
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong, H., Mason, S.P., Barabasi, A.L., and Oltvai, Z.N. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
15
-
-
0035853280
-
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
-
Landgraf, R., Xenarios, I., and Eisenberg, D. 2001. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol. 307: 1487-1502.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1487-1502
-
-
Landgraf, R.1
Xenarios, I.2
Eisenberg, D.3
-
16
-
-
0030447531
-
Protein clefts in molecular recognition and function
-
Laskowski, R.A., Luscombe, N.M., Swindells, M.B., and Thornton, J.M. 1996. Protein clefts in molecular recognition and function. Protein Sci. 5: 2438-2452.
-
(1996)
Protein Sci.
, vol.5
, pp. 2438-2452
-
-
Laskowski, R.A.1
Luscombe, N.M.2
Swindells, M.B.3
Thornton, J.M.4
-
17
-
-
0030659457
-
PDBsum: A Web-based database of summaries and analyses of all PDB structures
-
Laskowski, R.A., Hutchinson, E.G., Michie, A.D., Wallace, A.C., Jones, M.L., and Thornton, J.M. 1997. PDBsum: A Web-based database of summaries and analyses of all PDB structures. Trends Biochem. Sci. 22: 488-490.
-
(1997)
Trends Biochem. Sci.
, vol.22
, pp. 488-490
-
-
Laskowski, R.A.1
Hutchinson, E.G.2
Michie, A.D.3
Wallace, A.C.4
Jones, M.L.5
Thornton, J.M.6
-
18
-
-
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
-
19
-
-
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
-
20
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma, B., Elkayam, T., Wolfson, H., and Nussinov, R. 2003. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci. 100: 5772-5777.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
21
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.G., Brenner, S.E., Hubbard, T., and 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
-
22
-
-
0033588178
-
Non-active site changes elicit broad-based cross-resistance of the HIV-1 protease to inhibitors
-
Olsen, D.B., Stahlhut, M.W., Rutkowski, C.A., Schock, H.B., vanOlden, A.L., and Kuo, L.C. 1999. Non-active site changes elicit broad-based cross-resistance of the HIV-1 protease to inhibitors. J. Biol. Chem. 274: 23699-23701.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 23699-23701
-
-
Olsen, D.B.1
Stahlhut, M.W.2
Rutkowski, C.A.3
Schock, H.B.4
VanOlden, A.L.5
Kuo, L.C.6
-
23
-
-
0035940421
-
THEMATICS: A simple computational predictor of enzyme function from structure
-
Ondrechen, M.J., Clifton, J.G., and Ringe, D. 2001. THEMATICS: A simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. 98: 12473-12478.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 12473-12478
-
-
Ondrechen, M.J.1
Clifton, J.G.2
Ringe, D.3
-
24
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G., and Notredame, C. 2004. 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 340: 385-395.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
25
-
-
22444450449
-
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
-
Ota, N. and Agard, D.A. 2005. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J. Mol. Biol. 351: 345-354.
-
(2005)
J. Mol. Biol.
, vol.351
, pp. 345-354
-
-
Ota, N.1
Agard, D.A.2
-
26
-
-
1842454635
-
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contribution to drug resistance and a potential new target site for drugs
-
Perryman, A.L., Lin, J.-H., and McCammon, J.A. 2004. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contribution to drug resistance and a potential new target site for drugs. Protein Sci. 13: 1108-1123.
-
(2004)
Protein Sci.
, vol.13
, pp. 1108-1123
-
-
Perryman, A.L.1
Lin, J.-H.2
McCammon, J.A.3
-
27
-
-
0032422864
-
Use of propensities of amino acids to the local structure environment to understand effect of substitution mutations on protein stability
-
Reddy, B.V.B., Datta, S., and Tiguari, S. 1998. Use of propensities of amino acids to the local structure environment to understand effect of substitution mutations on protein stability. Protein Eng. 11: 1137-1145.
-
(1998)
Protein Eng.
, vol.11
, pp. 1137-1145
-
-
Reddy, B.V.B.1
Datta, S.2
Tiguari, S.3
-
28
-
-
0036306115
-
Why are proteins so robust to site mutations?
-
Taverna, D.M. and Goldstein, R.A. 2002. Why are proteins so robust to site mutations? J. Mol. Biol. 315: 479-484.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 479-484
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
29
-
-
0028197601
-
In vivo characterization of mutants of the bacteriophage f1 gene V protein isolated by saturation mutagenesis
-
Terwillinger, T.C., Zabin, H.B., Horvath, M.P., Sandberg, W.S., and Schlunk, P.M. 1994. In vivo characterization of mutants of the bacteriophage f1 gene V protein isolated by saturation mutagenesis. J. Mol. Biol. 236: 556-571.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 556-571
-
-
Terwillinger, T.C.1
Zabin, H.B.2
Horvath, M.P.3
Sandberg, W.S.4
Schlunk, P.M.5
-
30
-
-
14744305761
-
Using a library of structural templates to recognize catalytic sites and explore their evolution in homologous families
-
Torrance, J.M., Bartlett, G.J., Porter, C.T., and Thornton, J.M. 2005. Using a library of structural templates to recognize catalytic sites and explore their evolution in homologous families. J. Mol. Biol. 347: 565-581.
-
(2005)
J. Mol. Biol.
, vol.347
, pp. 565-581
-
-
Torrance, J.M.1
Bartlett, G.J.2
Porter, C.T.3
Thornton, J.M.4
-
31
-
-
33748138078
-
Protein-protein interfaces: Analysis of amino acid conservation in homodimers
-
Valdar, W.S.J. and Thornton, J.M. 2001. Protein-protein interfaces: Analysis of amino acid conservation in homodimers. Proteins 44: 150-165.
-
(2001)
Proteins
, vol.44
, pp. 150-165
-
-
Valdar, W.S.J.1
Thornton, J.M.2
-
32
-
-
41349118690
-
Smallworld view of the amino acids that play a key role in protein fold
-
Vendruscolo, M., Dokholyan, N.V., Paci, E., and Karplus, M. 2002. Smallworld view of the amino acids that play a key role in protein fold. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65: 0619101-0619104.
-
(2002)
Phys. Rev. E Stat. Nonlin. Soft Matter Phys.
, vol.65
, pp. 0619101-0619104
-
-
Vendruscolo, M.1
Dokholyan, N.V.2
Paci, E.3
Karplus, M.4
-
33
-
-
0032482432
-
Collective dynamics of small-world networks
-
Watts, D.J. and Strogatz, S.H. 1998. Collective dynamics of small-world networks. Nature 393: 440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
|