-
1
-
-
0031787022
-
100,000 protein structures for the biologist
-
Sali A. 100,000 protein structures for the biologist. Nature Struct. Biol. 5:1998;1029-1032.
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 1029-1032
-
-
Sali, A.1
-
2
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., 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.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
-
4
-
-
0033757840
-
From structure to function: Approaches and limitations
-
Thornton J.M., Todd A.E., Milburn D., Borkakoti N., Orengo C.A. From structure to function: approaches and limitations. Nature Struct. Biol. 7:2000;991-994.
-
(2000)
Nature Struct. Biol.
, vol.7
, pp. 991-994
-
-
Thornton, J.M.1
Todd, A.E.2
Milburn, D.3
Borkakoti, N.4
Orengo, C.A.5
-
5
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
6
-
-
0032944238
-
The PROSITE database, its status in 1999
-
Hofmann K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucl. Acids Res. 27:1999;215-219.
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 215-219
-
-
Hofmann, K.1
Bucher, P.2
Falquet, L.3
Bairoch, A.4
-
7
-
-
0031090688
-
Common fold, common function, common origin?
-
Suck D. Common fold, common function, common origin? Nature Struct. Biol. 4:1997;161-165.
-
(1997)
Nature Struct. Biol.
, vol.4
, pp. 161-165
-
-
Suck, D.1
-
9
-
-
0033597176
-
The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
-
Hegyi H., Gerstein M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288:1999;147-164.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 147-164
-
-
Hegyi, H.1
Gerstein, M.2
-
10
-
-
0034923923
-
Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
-
Gerlt J.A., Babbitt P.C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem. 70:2001;209-246.
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 209-246
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
11
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge O., Bourne H.R., Cohen F.E. 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.R.2
Cohen, F.E.3
-
12
-
-
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
-
13
-
-
0035896024
-
ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
-
Armon A., Graur D., Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 307:2001;447-463.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 447-463
-
-
Armon, A.1
Graur, D.2
Ben-Tal, N.3
-
14
-
-
0035126520
-
Prediction and confirmation of a site critical for effector regulation of RGS domain activity
-
Sowa M.E., He W., Slep K.C., Kercher M.A., Lichtarge O., Wensel T.G. Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nature Struct. Biol. 8:2001;234-237.
-
(2001)
Nature Struct. Biol.
, vol.8
, pp. 234-237
-
-
Sowa, M.E.1
He, W.2
Slep, K.C.3
Kercher, M.A.4
Lichtarge, O.5
Wensel, T.G.6
-
15
-
-
0033579464
-
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
-
Blom N., Gammeltoft S., Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294:1999;1351-1362.
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 1351-1362
-
-
Blom, N.1
Gammeltoft, S.2
Brunak, S.3
-
16
-
-
0034018755
-
Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network
-
Stahl M., Taroni C., Schneider G. Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network. Protein Eng. 13:2000;83-88.
-
(2000)
Protein Eng.
, vol.13
, pp. 83-88
-
-
Stahl, M.1
Taroni, C.2
Schneider, G.3
-
18
-
-
0031565729
-
Analysis of protein-protein interaction sites using surface patches
-
Jones S., Thornton J.M. Analysis of protein-protein interaction sites using surface patches. J. Mol. Biol. 272:1997;121-132.
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 121-132
-
-
Jones, S.1
Thornton, J.M.2
-
19
-
-
0034730415
-
A fast method to predict protein interaction sites from sequences
-
Gallet X., Charloteaux B., Thomas A., Brasseur R. A fast method to predict protein interaction sites from sequences. J. Mol. Biol. 302:2000;917-926.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 917-926
-
-
Gallet, X.1
Charloteaux, B.2
Thomas, A.3
Brasseur, R.4
-
20
-
-
0029973830
-
Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
-
Wallace A.C., Laskowski R.A., Thornton J.M. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5:1996;1001-1013.
-
(1996)
Protein Sci.
, vol.5
, pp. 1001-1013
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
21
-
-
0030724039
-
TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
-
Wallace A.C., Borkakoti N., Thornton J.M. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6:1997;2308-2323.
-
(1997)
Protein Sci.
, vol.6
, pp. 2308-2323
-
-
Wallace, A.C.1
Borkakoti, N.2
Thornton, J.M.3
-
22
-
-
0032483312
-
Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases
-
Fetrow J.S., Skolnick J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281:1998;949-968.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 949-968
-
-
Fetrow, J.S.1
Skolnick, J.2
-
23
-
-
0032843737
-
Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily
-
Fetrow J.S., Siew N., Skolnick J. Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. FASEB J. 13:1999;1866-1874.
-
(1999)
FASEB J.
, vol.13
, pp. 1866-1874
-
-
Fetrow, J.S.1
Siew, N.2
Skolnick, J.3
-
24
-
-
0035940421
-
THEMATICS: A simple computational predictor of enzyme function from structure
-
Ondrechen M.J., Clifton J.G., Ringe D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc. Natl Acad. Sci. USA. 98:2001;12473-12478.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 12473-12478
-
-
Ondrechen, M.J.1
Clifton, J.G.2
Ringe, D.3
-
25
-
-
12944331949
-
Predicting protein function from structure: Unique structural features of proteases
-
Stawiski E.W., Baucom A.E., Lohr S.C., Gregoret L.M. Predicting protein function from structure: unique structural features of proteases. Proc. Natl Acad. Sci. 97:2000;3954-3958.
-
(2000)
Proc. Natl Acad. Sci.
, vol.97
, pp. 3954-3958
-
-
Stawiski, E.W.1
Baucom, A.E.2
Lohr, S.C.3
Gregoret, L.M.4
-
26
-
-
0036364831
-
Progress in predicting protein function from structure: Unique features of O-glycosidase
-
Stawiski E.W., Mandel-Gutfreund Y., Gregoret L.M. Progress in predicting protein function from structure: unique features of O-glycosidase. Pacific Symp. Biocomput. 7:2002;637-648.
-
(2002)
Pacific Symp. Biocomput.
, vol.7
, pp. 637-648
-
-
Stawiski, E.W.1
Mandel-Gutfreund, Y.2
Gregoret, L.M.3
-
27
-
-
0022292404
-
Electrostatics and flexibility in protein-DNA interactions
-
Ohlendorf D.H., Matthew J.B. Electrostatics and flexibility in protein-DNA interactions. Advan. Biophys. 20:1985;137-151.
-
(1985)
Advan. Biophys.
, vol.20
, pp. 137-151
-
-
Ohlendorf, D.H.1
Matthew, J.B.2
-
29
-
-
0026682657
-
Transcription factors: Structural families and principles of DNA recognition
-
Pabo C.O., Sauer R.T. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61:1992;1053-1095.
-
(1992)
Annu. Rev. Biochem.
, vol.61
, pp. 1053-1095
-
-
Pabo, C.O.1
Sauer, R.T.2
-
30
-
-
0028839860
-
Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
-
Mandel-Gutfreund Y., Schueler O., Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. J. Mol. Biol. 253:1995;370-382.
-
(1995)
J. Mol. Biol.
, vol.253
, pp. 370-382
-
-
Mandel-Gutfreund, Y.1
Schueler, O.2
Margalit, H.3
-
33
-
-
0032787396
-
Implication of tubby proteins as transcription factors by structure-based functional analysis
-
Boggon T.J., Shan W.S., Santagata S., Myers S.C., Shapiro L. Implication of tubby proteins as transcription factors by structure-based functional analysis. Science. 286:1999;2119-2125.
-
(1999)
Science
, vol.286
, pp. 2119-2125
-
-
Boggon, T.J.1
Shan, W.S.2
Santagata, S.3
Myers, S.C.4
Shapiro, L.5
-
34
-
-
0034702838
-
Membrane binding of peptides containing both basic and aromatic residues. Experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of MARCKS
-
Arbuzova A., Wang L., Wang J., Hangyás-Mihályné G., Murray D., Honig B., McLaughlin S. Membrane binding of peptides containing both basic and aromatic residues. Experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of MARCKS. Biochemistry. 39:2000;10330-10339.
-
(2000)
Biochemistry
, vol.39
, pp. 10330-10339
-
-
Arbuzova, A.1
Wang, L.2
Wang, J.3
Hangyás-Mihályné, G.4
Murray, D.5
Honig, B.6
McLaughlin, S.7
-
35
-
-
0034634628
-
The relaxin receptor-binding site geometry suggests a novel gripping mode of interaction
-
Büllesbach E.E., Schwabe C. The relaxin receptor-binding site geometry suggests a novel gripping mode of interaction. J. Biol. Chem. 275:2000;35276-35280.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 35276-35280
-
-
Büllesbach, E.E.1
Schwabe, C.2
-
37
-
-
0000732609
-
GRASP: Graphical representation and analysis of surface properties
-
Nicholls A., Bharadwaj R., Honig B. GRASP: graphical representation and analysis of surface properties. Biophys. J. 64:1993.
-
(1993)
Biophys. J.
, vol.64
-
-
Nicholls, A.1
Bharadwaj, R.2
Honig, B.3
-
39
-
-
0025195188
-
The cytochrome P-450cam binding surface as defined by site-directed mutagenesis and electrostatic modeling
-
Stayton P.S., Sligar S.G. The cytochrome P-450cam binding surface as defined by site-directed mutagenesis and electrostatic modeling. Biochemistry. 29:1990;7381-7386.
-
(1990)
Biochemistry
, vol.29
, pp. 7381-7386
-
-
Stayton, P.S.1
Sligar, S.G.2
-
40
-
-
0028351539
-
Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate
-
Belrhali H., Yaremchuk A., Tukalo M., Larsen K., Berthet-Colominas C., Leberman R., et al. Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Science. 263:1994;1432-1436.
-
(1994)
Science
, vol.263
, pp. 1432-1436
-
-
Belrhali, H.1
Yaremchuk, A.2
Tukalo, M.3
Larsen, K.4
Berthet-Colominas, C.5
Leberman, R.6
-
41
-
-
0033150942
-
From protein sequence to function
-
Danchin A. From protein sequence to function. Curr. Opin. Struct. Biol. 9:1999;363-367.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 363-367
-
-
Danchin, A.1
-
44
-
-
0033573827
-
Structural features of protein-nucleic acid recognition sites
-
Nadassy K., Wodak S.J., Janin J. Structural features of protein-nucleic acid recognition sites. Biochemistry. 38:1999;1999-2017.
-
(1999)
Biochemistry
, vol.38
, pp. 1999-2017
-
-
Nadassy, K.1
Wodak, S.J.2
Janin, J.3
-
45
-
-
0028204490
-
Do salt bridges stabilize proteins? A continuum electrostatic analysis
-
Hendsch Z.S., Tidor B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3:1994;211-226.
-
(1994)
Protein Sci.
, vol.3
, pp. 211-226
-
-
Hendsch, Z.S.1
Tidor, B.2
-
46
-
-
0022347081
-
Fractal surfaces of proteins
-
Lewis M., Rees D.C. Fractal surfaces of proteins. Science. 230:1985;1163-1165.
-
(1985)
Science
, vol.230
, pp. 1163-1165
-
-
Lewis, M.1
Rees, D.C.2
-
47
-
-
0035865891
-
Protein-RNA interactions: A structural analysis
-
Jones S., Daley D.T., Luscombe N.M., Berman H.M., Thornton J.M. Protein-RNA interactions: a structural analysis. Nucl. Acids Res. 29:2001;943-954.
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 943-954
-
-
Jones, S.1
Daley, D.T.2
Luscombe, N.M.3
Berman, H.M.4
Thornton, J.M.5
-
48
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
see also pp. 307-328
-
Laskowski R.A. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 13:1995;323-330. see also pp. 307-328.
-
(1995)
J. Mol. Graph.
, vol.13
, pp. 323-330
-
-
Laskowski, R.A.1
-
50
-
-
0036300444
-
Structural clusters of evolutionary trace residues are statistically significant and common in proteins
-
Madabushi S., Yao H., Marsh M., Kristensen D.M., Philippi A., Sowa M.E., 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.M.4
Philippi, A.5
Sowa, M.E.6
Lichtarge, O.7
-
51
-
-
0036468670
-
Evolutionary predictions of binding surfaces and interactions
-
Lichtarge O., Sowa M.E. 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.E.2
-
52
-
-
0036074510
-
Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
-
Luscombe N.M., Thornton J.M. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol. 320:2002;991-1009.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
53
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaeffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. 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.F.1
Madden, T.L.2
Schaeffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
54
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews B.W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta. 405:1975;442-451.
-
(1975)
Biochim. Biophys. Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
55
-
-
0034682882
-
Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
-
Pabo C.O., Nekludova L. Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol. 301:2000;597-624.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 597-624
-
-
Pabo, C.O.1
Nekludova, L.2
-
56
-
-
0028773281
-
A framework for the DNA-protein recognition code of the probe helix in transcription factors: The chemical and stereochemical rules
-
Suzuki M. A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules. Structure. 2:1994;317-326.
-
(1994)
Structure
, vol.2
, pp. 317-326
-
-
Suzuki, M.1
-
58
-
-
0026742978
-
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
-
Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., et al. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759.
-
(1992)
Biophys. J.
, vol.63
, pp. 751-759
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, J.4
Gelbin, A.5
Demeny, T.6
-
59
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 3:1994;522-524.
-
(1994)
Protein Sci.
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
60
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:1994;777-793.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
61
-
-
33645941402
-
The OPLS potential functions for proteins. Energy minimization for crystals of cyclic peptides and crambin
-
Jorgensen W.L., Tirado-Rives J. The OPLS potential functions for proteins. Energy minimization for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1988;1657-1666.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
63
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
64
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee B., Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
65
-
-
0001073978
-
A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites
-
Gerstein M. A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites. Acta Crystallog. 48:1992;271-276.
-
(1992)
Acta Crystallog.
, vol.48
, pp. 271-276
-
-
Gerstein, M.1
|