-
1
-
-
0033970022
-
Expectations from structural genomics
-
Brenner,S.E. and Levitt,M. (2000) Expectations from structural genomics. Protein Sci., 9, 197-200.
-
(2000)
Protein Sci.
, vol.9
, pp. 197-200
-
-
Brenner, S.E.1
Levitt, M.2
-
2
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
Martin, M.J.7
Michoud, K.8
O'Donovan, C.9
Phan, I.10
-
3
-
-
0036081345
-
GenBank
-
Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J., Rapp,B.A. and Wheeler,D.L. (2002) GenBank. Nucleic Acids Res., 30, 17-20.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 17-20
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Rapp, B.A.5
Wheeler, D.L.6
-
4
-
-
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, 58, 899-907.
-
(2002)
Acta Crystallogr. D
, 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
-
5
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker,D. and Sali,A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
6
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom,M.A., Stuart,A.C., Fiser,A., Sanchez,R., Melo,F. and Sali,A. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291-325.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
7
-
-
0036089481
-
MODBASE, a database of annotated comparative protein structure models
-
Pieper,U., Eswar,N., Stuart,A.C., Ilyin,V.A. and Sali,A. (2002) MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res., 30, 255-259.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 255-259
-
-
Pieper, U.1
Eswar, N.2
Stuart, A.C.3
Ilyin, V.A.4
Sali, A.5
-
8
-
-
0035698589
-
CAFASP2: The second critical assessment of fully automated structure prediction methods
-
Fischer,D., Elofsson,A., Rychlewski,L., Pazos,F., Valencia,A., Rost,B., Ortiz,A.R. and Dunbrack,R.L.,Jr (2001) CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins (Suppl. 5), 171-183.
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 171-183
-
-
Fischer, D.1
Elofsson, A.2
Rychlewski, L.3
Pazos, F.4
Valencia, A.5
Rost, B.6
Ortiz, A.R.7
Dunbrack Jr., R.L.8
-
9
-
-
0043123211
-
EVA: Evaluation of protein structure prediction servers
-
Koh,I.Y.Y., Eyrich,V.A., Marti-Renom,M.A., Przybylski,D., Madhusudhan,M.S., Eswar,N., Grana,O., Pazos,F., Valencia,A., Sali,A. et al. (2003) EVA: evaluation of protein structure prediction servers. Nucleic Acids Res., 31, 3311-3315.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3311-3315
-
-
Koh, I.Y.Y.1
Eyrich, V.A.2
Marti-Renom, M.A.3
Przybylski, D.4
Madhusudhan, M.S.5
Eswar, N.6
Grana, O.7
Pazos, F.8
Valencia, A.9
Sali, A.10
-
10
-
-
0035698724
-
LiveBench-2: Large-scale automated evaluation of protein structure prediction servers
-
Bujnicki,J.M., Elofsson,A., Fischer,D. and Rychlewski,L. (2001) LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins (Suppl. 5), 184-191.
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 184-191
-
-
Bujnicki, J.M.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
11
-
-
0034853119
-
DBAli: A database of protein structure alignments
-
Marti-Renom,M.A., Ilyin,V.A. and Sali,A. (2001) DBAli: a database of protein structure alignments. Bioinformatics, 17, 746-747.
-
(2001)
Bioinformatics
, vol.17
, pp. 746-747
-
-
Marti-Renom, M.A.1
Ilyin, V.A.2
Sali, A.3
-
12
-
-
0346882663
-
ModLoop: Automated modeling of loops in protein structures
-
in press
-
Fiser,A. and Sali,A. (2003) ModLoop: Automated modeling of loops in protein structures. Bioinformatics, in press.
-
(2003)
Bioinformatics
-
-
Fiser, A.1
Sali, A.2
-
13
-
-
0000577528
-
CHIMERA: An extensible molecular modeling application constructed using standard components
-
Huang,C.C., Couch,G.S., Pettersen,E.F. and Ferring,T.E. (1996) CHIMERA: An extensible molecular modeling application constructed using standard components. Pacific Symp. Biocomput., 1, 724.
-
(1996)
Pacific Symp. Biocomput.
, vol.1
, pp. 724
-
-
Huang, C.C.1
Couch, G.S.2
Pettersen, E.F.3
Ferring, T.E.4
-
14
-
-
0348121087
-
-
Molecular Simulations Inc
-
2. Molecular Simulations Inc., Vol. 2, p. 5.
-
(1995)
2
, vol.2
, pp. 5
-
-
Sali, A.1
-
15
-
-
0036129154
-
Structural Genomics: A pipeline for providing structures for the biologist
-
Chance,M.R., Bresnick,A.R., Burley,S.K., Jiang,J.S., Lima,C.D.S.A., Almo,S.C., Bonanno,J.B., Buglino,J.A., Boulton,S., Chen,H. et al. (2002) Structural Genomics: A pipeline for providing structures for the biologist. Protein Sci., 11, 723-738.
-
(2002)
Protein Sci.
, vol.11
, pp. 723-738
-
-
Chance, M.R.1
Bresnick, A.R.2
Burley, S.K.3
Jiang, J.S.4
Lima, C.D.S.A.5
Almo, S.C.6
Bonanno, J.B.7
Buglino, J.A.8
Boulton, S.9
Chen, H.10
-
16
-
-
0043123167
-
Tools for comparative protein structure modeling and analysis
-
Eswar,N., John,B., Mirkovic,N., Fiser,A., Ilyin,V., Pieper,U., Stuart,A.C., Marti-Renom,M.A., Madhusudhan,M.S., Yerkovich,B. et al. (2003) Tools for comparative protein structure modeling and analysis. Nucleic Acids Res., 31, 3375-3380.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3375-3380
-
-
Eswar, N.1
John, B.2
Mirkovic, N.3
Fiser, A.4
Ilyin, V.5
Pieper, U.6
Stuart, A.C.7
Marti-Renom, M.A.8
Madhusudhan, M.S.9
Yerkovich, B.10
-
17
-
-
0036139410
-
EVA: Continuous automatic evaluation of protein structure prediction servers
-
Eyrich,V.A., Marti-Renom,M.A., Przybylski,D., Madhusudhan,M.S., Fiser,A., Pazos,F., Valencia,A., Sali,A. and Rost,B. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242-1243.
-
(2001)
Bioinformatics
, vol.17
, pp. 1242-1243
-
-
Eyrich, V.A.1
Marti-Renom, M.A.2
Przybylski, D.3
Madhusudhan, M.S.4
Fiser, A.5
Pazos, F.6
Valencia, A.7
Sali, A.8
Rost, B.9
-
18
-
-
0141978673
-
Comparative protein structure modeling by iterative alignment, model building and model assessment
-
John,B. and Sali,A. (2003) Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res., 31, 3982-3992.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3982-3992
-
-
John, B.1
Sali, A.2
-
19
-
-
0141448942
-
ModBase: A database of comparative protein structure models
-
Sanchez,R. and Sali,A. (1999) ModBase: a database of comparative protein structure models. Bioinformatics, 15, 1060-1061.
-
(1999)
Bioinformatics
, vol.15
, pp. 1060-1061
-
-
Sanchez, R.1
Sali, A.2
-
20
-
-
0343920731
-
MODBASE, a database of annotated comparative protein structure models
-
Sanchez,R., Pieper,U., Mirkovic,N., de Bakker,P.I., Wittenstein,E. and Sali,A. (2000) MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res., 28, 250-253.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 250-253
-
-
Sanchez, R.1
Pieper, U.2
Mirkovic, N.3
de Bakker, P.I.4
Wittenstein, E.5
Sali, A.6
-
21
-
-
0025317502
-
Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
-
Sali,A. and Blundell,T.L. (1990) Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol., 212, 403-428.
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 403-428
-
-
Sali, A.1
Blundell, T.L.2
-
22
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
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.
-
(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
-
23
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
Sadreyev,R. and Grishin,N. (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
24
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
25
-
-
0036145846
-
Statistical potentials for fold assessment
-
Melo,F., Sanchez,R. and Sali,A. (2002) Statistical potentials for fold assessment. Protein Sci., 11, 430-448.
-
(2002)
Protein Sci.
, vol.11
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
26
-
-
0038438514
-
IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
-
Schaffer,A.A., Wolf,Y.I., Ponting,C.P., Koonin,E.V., Aravind,L. and Altschul,S.F. (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 15, 1000-1011.
-
(1999)
Bioinformatics
, vol.15
, pp. 1000-1011
-
-
Schaffer, A.A.1
Wolf, Y.I.2
Ponting, C.P.3
Koonin, E.V.4
Aravind, L.5
Altschul, S.F.6
-
27
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Marcotte,E.M., Pellegrini,M., Thompson,M.J., Yeates,T.O. and Eisenberg,D. (1999) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
28
-
-
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
-
29
-
-
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
-
30
-
-
0036169142
-
LigBase: A database of families of aligned ligand binding sites in known protein sequences and structures
-
Stuart,A.C., Ilyin,V.A. and Sali,A. (2002) LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics, 18, 200-201.
-
(2002)
Bioinformatics
, vol.18
, pp. 200-201
-
-
Stuart, A.C.1
Ilyin, V.A.2
Sali, A.3
-
31
-
-
0034995092
-
Completeness in structural genomics
-
Vitkup,D., Melamud,E., Moult,J. and Sander,C. (2001) Completeness in structural genomics. Nature Struct. Biol., 8, 559-566.
-
(2001)
Nature Struct. Biol.
, vol.8
, pp. 559-566
-
-
Vitkup, D.1
Melamud, E.2
Moult, J.3
Sander, C.4
-
32
-
-
0037265212
-
The CATH domain structure database
-
Orengo,C.A., Pearl,F.M. and Thornton,J.M. (2003) The CATH domain structure database. Methods Biochem. Anal., 44, 249-271.
-
(2003)
Methods Biochem. Anal.
, vol.44
, pp. 249-271
-
-
Orengo, C.A.1
Pearl, F.M.2
Thornton, J.M.3
-
33
-
-
0011542799
-
The Pfam protein families database
-
Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
34
-
-
0000120520
-
ProDom: Automated clustering of homologous domains
-
Servant,F., Bru,C., Carrere,S., Courcelle,E., Gouzy,J., Peyruc,D. and Kahn,D. (2002) ProDom: automated clustering of homologous domains. Brief. Bioinform., 3, 246-251.
-
(2002)
Brief. Bioinform.
, vol.3
, pp. 246-251
-
-
Servant, F.1
Bru, C.2
Carrere, S.3
Courcelle, E.4
Gouzy, J.5
Peyruc, D.6
Kahn, D.7
-
35
-
-
0037250168
-
The UCSC Genome Browser Database
-
Karolchik,D., Baertsch,R., Diekhans,M., Furey,T.S., Hinrichs,A., Lu,Y.T., Roskin,K.M., Schwartz,M., Sugnet,C.W., Thomas,D.J. et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51-54.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 51-54
-
-
Karolchik, D.1
Baertsch, R.2
Diekhans, M.3
Furey, T.S.4
Hinrichs, A.5
Lu, Y.T.6
Roskin, K.M.7
Schwartz, M.8
Sugnet, C.W.9
Thomas, D.J.10
|