-
1
-
-
17844392864
-
Combining prediction of secondary structure and solvent accessibility in proteins
-
Adamczak, R., Porollo, A., and Meller, J. 2005. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 59: 467-475.
-
(2005)
Proteins
, vol.59
, pp. 467-475
-
-
Adamczak, R.1
Porollo, A.2
Meller, J.3
-
2
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy, P. and Russell, R.B. 2002. Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. 99: 5896-5901.
-
(2002)
Proc. Natl. Acad. Sci
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
3
-
-
0037250158
-
InterPreTS: Protein interaction prediction through tertiary structure
-
Aloy, P. and Russell, R.B. 2003. InterPreTS: Protein interaction prediction through tertiary structure. Bioinformatics 19: 161-162.
-
(2003)
Bioinformatics
, vol.19
, pp. 161-162
-
-
Aloy, P.1
Russell, R.B.2
-
4
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
doi: 10.1093/nar/25.17.3389
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. doi: 10.1093/nar/25.17.3389.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
5
-
-
20844454090
-
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
-
Aytuna, A.S., Gursoy, A., and Keskin, O. 2005. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21: 2850-2855.
-
(2005)
Bioinformatics
, vol.21
, pp. 2850-2855
-
-
Aytuna, A.S.1
Gursoy, A.2
Keskin, O.3
-
6
-
-
0036616218
-
The Protein Data Bank
-
Berman, H.M., Battistuz, T., Bhat, T.N., Bluhm, W.F., Bourne, P.E., Burkhardt, K., Feng, Z., Gilliland, G.L., Iype, L., Jain, S., et al. 2002. The Protein Data Bank. Acta Crystallogr. D Biol. Crystallogr. 58: 899-907.
-
(2002)
Acta Crystallogr. D Biol. Crystallogr
, vol.58
, pp. 899-907
-
-
Berman, H.M.1
Battistuz, T.2
Bhat, T.N.3
Bluhm, W.F.4
Bourne, P.E.5
Burkhardt, K.6
Feng, Z.7
Gilliland, G.L.8
Iype, L.9
Jain, S.10
-
7
-
-
38649142924
-
Threading algorithms
-
eds. M. Dunn et al, pp, J. Wiley, Hoboken, NJ
-
Bienkowska, J. and Lathrop, R. 2005. Threading algorithms. In Encyclopedia of genetics, genomics, proteomics, and bioinformatics (eds. M. Dunn et al.), pp. 3555-3568. J. Wiley, Hoboken, NJ.
-
(2005)
Encyclopedia of genetics, genomics, proteomics, and bioinformatics
, pp. 3555-3568
-
-
Bienkowska, J.1
Lathrop, R.2
-
8
-
-
33744944082
-
Interactions of tumor necrosis factor (TNF) and TNF receptor family members in the mouse and human
-
Bossen, C., Ingold, K., Tardivel, A., Bodmer, J.L., Gaide, O., Hertig, S., Ambrose, C., Tschopp, J., and Schneider, P. 2006. Interactions of tumor necrosis factor (TNF) and TNF receptor family members in the mouse and human. J. Biol. Chem. 281: 13964-13971.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 13964-13971
-
-
Bossen, C.1
Ingold, K.2
Tardivel, A.3
Bodmer, J.L.4
Gaide, O.5
Hertig, S.6
Ambrose, C.7
Tschopp, J.8
Schneider, P.9
-
9
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie, J.U., Luthy, R., and Eisenberg, D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
10
-
-
0346733329
-
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
-
Caffrey, D.R., Somaroo, S., Hughes, J.D., Mintseris, J., and Huang, E.S. 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
-
11
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu, A.A., Shelenkov, A.A., and Dunbrack Jr., R.L. 2003. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12: 2001-2014.
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack Jr., R.L.3
-
12
-
-
18744382508
-
PIBASE: A comprehensive database of structurally defined protein interfaces
-
Davis, F.P. and Sali, A. 2005. PIBASE: A comprehensive database of structurally defined protein interfaces. Bioinformatics 21: 1901-1907.
-
(2005)
Bioinformatics
, vol.21
, pp. 1901-1907
-
-
Davis, F.P.1
Sali, A.2
-
13
-
-
33745142940
-
Protein complex compositions predicted by structural similarity
-
doi: 10.1093/nar/gkl353
-
Davis, F.P., Braberg, H., Shen, M.Y., Pieper, U., Sali, A., and Madhusudhan, M.S. 2006. Protein complex compositions predicted by structural similarity. Nucleic Acids Res. 34: 2943-2952. doi: 10.1093/nar/gkl353.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2943-2952
-
-
Davis, F.P.1
Braberg, H.2
Shen, M.Y.3
Pieper, U.4
Sali, A.5
Madhusudhan, M.S.6
-
14
-
-
0033654768
-
Hybrid fold recognition: Combining sequence derived properties with evolutionary information
-
Fischer, D. 2000. Hybrid fold recognition: Combining sequence derived properties with evolutionary information. Pac. Symp. Biocomput. 5: 119-130.
-
(2000)
Pac. Symp. Biocomput
, vol.5
, pp. 119-130
-
-
Fischer, D.1
-
15
-
-
0034595516
-
Co-evolution of proteins with their interaction partners
-
Goh, C.S., Bogan, A.A., Joachimiak, M., Walther, D., and Cohen, F.E. 2000. Co-evolution of proteins with their interaction partners. J. Mol. Biol. 299: 283-293.
-
(2000)
J. Mol. Biol
, vol.299
, pp. 283-293
-
-
Goh, C.S.1
Bogan, A.A.2
Joachimiak, M.3
Walther, D.4
Cohen, F.E.5
-
16
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89: 10915-10919.
-
(1992)
Proc. Natl. Acad. Sci
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
17
-
-
0024234855
-
CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
-
Higgins, D.G. and Sharp, P.M. 1988. CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 73: 237-244.
-
(1988)
Gene
, vol.73
, pp. 237-244
-
-
Higgins, D.G.1
Sharp, P.M.2
-
18
-
-
0033212968
-
Triggering cell death: The crystal structure of Apo2L/TRAIL in a complex with death receptor 5
-
Hymowitz, S.G., Christinger, H.W., Fuh, G., Ultsch, M., O'Connell, M., Kelley, R.F., Ashkenazi, A., and de Vos, A.M. 1999. Triggering cell death: The crystal structure of Apo2L/TRAIL in a complex with death receptor 5. Mol. Cell 4: 563-571.
-
(1999)
Mol. Cell
, vol.4
, pp. 563-571
-
-
Hymowitz, S.G.1
Christinger, H.W.2
Fuh, G.3
Ultsch, M.4
O'Connell, M.5
Kelley, R.F.6
Ashkenazi, A.7
de Vos, A.M.8
-
19
-
-
13244262600
-
Assessing predictions of protein-protein interaction: The CAPRI experiment
-
Janin, J. 2005. Assessing predictions of protein-protein interaction: The CAPRI experiment. Protein Sci. 14: 278-283.
-
(2005)
Protein Sci
, vol.14
, pp. 278-283
-
-
Janin, J.1
-
20
-
-
0033537993
-
GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
-
Jones, D.T. 1999. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287: 797-815.
-
(1999)
J. Mol. Biol
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
21
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. A new approach to protein fold recognition. Nature 358: 86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
22
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
23
-
-
0033665510
-
BALL - rapid software prototyping in computational molecular biology. Biochemicals algorithms library
-
Kohlbacher, O. and Lenhof, H.P. 2000. BALL - rapid software prototyping in computational molecular biology. Biochemicals algorithms library. Bioinformatics 16: 815-824.
-
(2000)
Bioinformatics
, vol.16
, pp. 815-824
-
-
Kohlbacher, O.1
Lenhof, H.P.2
-
24
-
-
0029912991
-
Global optimum protein threading with gapped alignment and empirical pair score functions
-
Lathrop, R.H. and Smith, T.F. 1996. Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol. 255: 641-665.
-
(1996)
J. Mol. Biol
, vol.255
, pp. 641-665
-
-
Lathrop, R.H.1
Smith, T.F.2
-
25
-
-
0032212028
-
A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment
-
Lathrop, R.H., Rogers Jr., R.G., Smith, T.F., and White, J.V. 1998. A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment. Bull. Math. Biol. 60: 1039-1071.
-
(1998)
Bull. Math. Biol
, vol.60
, pp. 1039-1071
-
-
Lathrop, R.H.1
Rogers Jr., R.G.2
Smith, T.F.3
White, J.V.4
-
26
-
-
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
-
27
-
-
0037110589
-
MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
-
Lu, L., Lu, H., and Skolnick, J. 2002. MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49: 350-364.
-
(2002)
Proteins
, vol.49
, pp. 350-364
-
-
Lu, L.1
Lu, H.2
Skolnick, J.3
-
28
-
-
0037340493
-
Development of unified statistical potentials describing protein-protein interactions
-
Lu, H., Lu, L., and Skolnick, J. 2003. Development of unified statistical potentials describing protein-protein interactions. Biophys. J. 84: 1895-1901.
-
(2003)
Biophys. J
, vol.84
, pp. 1895-1901
-
-
Lu, H.1
Lu, L.2
Skolnick, J.3
-
29
-
-
0038021436
-
Assessment of blind predictions of protein-protein interactions: Current status of docking methods
-
Mendez, R., Leplae, R., De Maria, L., and Wodak, S.J. 2003. Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins 52: 51-67.
-
(2003)
Proteins
, vol.52
, pp. 51-67
-
-
Mendez, R.1
Leplae, R.2
De Maria, L.3
Wodak, S.J.4
-
30
-
-
0000229628
-
A system for induction of oblique decision trees
-
Murthy, S., Kasif, S., and Saltzberg, S. 1994. A system for induction of oblique decision trees. J. Artif. Intell. Res. 2: 1-32.
-
(1994)
J. Artif. Intell. Res
, vol.2
, pp. 1-32
-
-
Murthy, S.1
Kasif, S.2
Saltzberg, S.3
-
31
-
-
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
-
32
-
-
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
-
33
-
-
0034628922
-
Combination of threading potentials and sequence profiles improves fold recognition
-
Panchenko, A.R., Marchler-Bauer, A., and Bryant, S.H. 2000. Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol. 296: 1319-1331.
-
(2000)
J. Mol. Biol
, vol.296
, pp. 1319-1331
-
-
Panchenko, A.R.1
Marchler-Bauer, A.2
Bryant, S.H.3
-
34
-
-
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
-
35
-
-
9644262469
-
Interferons, interferon-like cytokines, and their receptors
-
Pestka, S., Krause, C.D., and Walter, M.R. 2004. Interferons, interferon-like cytokines, and their receptors. Immunol. Rev. 202: 8-32.
-
(2004)
Immunol. Rev
, vol.202
, pp. 8-32
-
-
Pestka, S.1
Krause, C.D.2
Walter, M.R.3
-
36
-
-
33644874394
-
MODBASE: A database of annotated comparative protein structure models and associated resources
-
doi: 10.1093/nar/gkj059
-
Pieper, U., Eswar, N., Davis, F.P., Braberg, H., Madhusudhan, M.S., Rossi, A., Marti-Renom, M., Karchin, R., Webb, B.M., Eramian, D., et al. 2006. MODBASE: A database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34: D291-D295. doi: 10.1093/nar/gkj059.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Pieper, U.1
Eswar, N.2
Davis, F.P.3
Braberg, H.4
Madhusudhan, M.S.5
Rossi, A.6
Marti-Renom, M.7
Karchin, R.8
Webb, B.M.9
Eramian, D.10
-
37
-
-
0242443693
-
Force fields for protein simulations
-
Ponder, J.W. and Case, D.A. 2003. Force fields for protein simulations. Adv. Protein Chem. 66: 27-85.
-
(2003)
Adv. Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
38
-
-
3442901082
-
Improving fold recognition without folds
-
Przybylski, D. and Rost, B. 2004. Improving fold recognition without folds. J. Mol. Biol. 341: 255-269.
-
(2004)
J. Mol. Biol
, vol.341
, pp. 255-269
-
-
Przybylski, D.1
Rost, B.2
-
39
-
-
15944418607
-
Random forest similarity for protein-protein interaction prediction from multiple sources
-
Qi, Y., Klein-Seetharaman, J., and Bar-Joseph, Z. 2005. Random forest similarity for protein-protein interaction prediction from multiple sources. Pac. Symp. Biocomput. 531-542.
-
(2005)
Pac. Symp. Biocomput
, pp. 531-542
-
-
Qi, Y.1
Klein-Seetharaman, J.2
Bar-Joseph, Z.3
-
40
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
-
(1987)
Mol. Biol. Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
41
-
-
39049191929
-
Struct2Net: Integrating structureInto protein-protein interaction prediction
-
Singh, R., Xu, J., and Berger, B. 2006. Struct2Net: Integrating structureInto protein-protein interaction prediction. Pac. Symp. Biocomput. 11: 403-414.
-
(2006)
Pac. Symp. Biocomput
, vol.11
, pp. 403-414
-
-
Singh, R.1
Xu, J.2
Berger, B.3
-
42
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith, G.R. and Sternberg, M.J. 2002. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12: 28-35.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.2
-
43
-
-
24644464131
-
An atomic environment potential for use in protein structure prediction
-
Summa, C.M., Levitt, M., and Degrado, W.F. 2005. An atomic environment potential for use in protein structure prediction. J. Mol. Biol. 352: 986-1001.
-
(2005)
J. Mol. Biol
, vol.352
, pp. 986-1001
-
-
Summa, C.M.1
Levitt, M.2
Degrado, W.F.3
-
44
-
-
3242892063
-
ADVICE: Automated detection and validation of interaction by co-evolution
-
doi: 10.1093/nar/gkh471
-
Tan, S.H., Zhang, Z., and Ng, S.K. 2004. ADVICE: Automated detection and validation of interaction by co-evolution. Nucleic Acids Res. 32: W69-W72. doi: 10.1093/nar/gkh471.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Tan, S.H.1
Zhang, Z.2
Ng, S.K.3
-
46
-
-
33644876493
-
SCOPPI: A structural classification of protein-protein interfaces
-
doi: 10.1093/nar/gkj099
-
Winter, C., Henschel, A., Kim, W.K., and Schroeder, M. 2006. SCOPPI: A structural classification of protein-protein interfaces. Nucleic Acids Res. 34: D310-D314. doi: 10.1093/nar/gkj099.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Winter, C.1
Henschel, A.2
Kim, W.K.3
Schroeder, M.4
-
47
-
-
0242369082
-
RAPTOR: Optimal protein threading by linear programming
-
Xu, J., Li, M., Kim, D., and Xu, Y. 2003a. RAPTOR: Optimal protein threading by linear programming. J. Bioinform. Comput. Biol. 1: 95-117.
-
(2003)
J. Bioinform. Comput. Biol
, vol.1
, pp. 95-117
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
-
48
-
-
0037731050
-
Protein threading by linear programming
-
Xu, J., Li, M., Lin, G., Kim, D., and Xu, Y. 2003b. Protein threading by linear programming. Pac. Symp. Biocomput. 8: 264-275.
-
(2003)
Pac. Symp. Biocomput
, vol.8
, pp. 264-275
-
-
Xu, J.1
Li, M.2
Lin, G.3
Kim, D.4
Xu, Y.5
-
49
-
-
19544388989
-
Multiple flexible structure alignment using partial order graphs
-
Ye, Y. and Godzik, A. 2005. Multiple flexible structure alignment using partial order graphs. Bioinformatics 21: 2362-2369.
-
(2005)
Bioinformatics
, vol.21
, pp. 2362-2369
-
-
Ye, Y.1
Godzik, A.2
-
50
-
-
30344488120
-
TASSER: An automated method for the prediction of protein tertiary structures in CASP6
-
Zhang, Y., Arakaki, A.K., and Skolnick, J. 2005. TASSER: An automated method for the prediction of protein tertiary structures in CASP6. Proteins (Suppl. 7) 61: 91-98.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
|