-
1
-
-
0034126813
-
Protein structure prediction in the postgenomic era
-
Jones DT. Protein structure prediction in the postgenomic era. Curr Opin Struct Biol 2000;10:371-379.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 371-379
-
-
Jones, D.T.1
-
2
-
-
0038438514
-
IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
-
Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 1999;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
-
3
-
-
0029174347
-
Multiple alignment using hidden Markov models
-
Eddy SR. Multiple alignment using hidden Markov models. Proc Intl Conf Intell Syst Mol Biol 1995;3:114-1120.
-
(1995)
Proc Intl Conf Intell Syst Mol Biol
, vol.3
, pp. 114-1120
-
-
Eddy, S.R.1
-
4
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
5
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;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
-
6
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Intl Conf Intell Syst Mol Biol 1994;2:28-36.
-
(1994)
Proc Intl Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
7
-
-
0029159799
-
Finding flexible patterns in unaligned protein sequences
-
Jonassen I, Collins JF, Higgins DG. Finding flexible patterns in unaligned protein sequences. Protein Sci 1995;4:1587-1595.
-
(1995)
Protein Sci
, vol.4
, pp. 1587-1595
-
-
Jonassen, I.1
Collins, J.F.2
Higgins, D.G.3
-
8
-
-
0034123819
-
SPLASH: Structural pattern localization analysis by sequential histograms
-
Califano A. SPLASH: structural pattern localization analysis by sequential histograms. Bioinformatics 2000;16:341-357.
-
(2000)
Bioinformatics
, vol.16
, pp. 341-357
-
-
Califano, A.1
-
9
-
-
0029144601
-
Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
-
Neuwald AF, Liu JS, Lawrence CE. Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 1995;4:1618-1632.
-
(1995)
Protein Sci
, vol.4
, pp. 1618-1632
-
-
Neuwald, A.F.1
Liu, J.S.2
Lawrence, C.E.3
-
10
-
-
0025882349
-
PROSITE: A dictionary of sites and patterns in proteins
-
Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res 1991;19(Suppl):2241-2245.
-
(1991)
Nucleic Acids Res
, vol.19
, Issue.SUPPL.
, pp. 2241-2245
-
-
Bairoch, A.1
-
11
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127-134.
-
(1995)
Protein Eng
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
12
-
-
0032475938
-
Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity
-
Fetrow JS, Godzik A, Skolnick J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J Mol Biol 1998;282:703-711.
-
(1998)
J Mol Biol
, vol.282
, pp. 703-711
-
-
Fetrow, J.S.1
Godzik, A.2
Skolnick, J.3
-
13
-
-
0031844330
-
Fold and function predictions for Mycoplasma genitalium proteins
-
Rychlewski L, Zhang B, Godzik A. Fold and function predictions for Mycoplasma genitalium proteins. Fold Des 1998;3:229-238.
-
(1998)
Fold Des
, vol.3
, pp. 229-238
-
-
Rychlewski, L.1
Zhang, B.2
Godzik, A.3
-
14
-
-
0035782660
-
Enhanced functional annotation of protein sequences via the use of structural descriptors
-
Di Gennaro JA, Siew N, Hoffman BT, Zhang L, Skolnick J, Neilson LI, Fetrow JS. Enhanced functional annotation of protein sequences via the use of structural descriptors. J Struct Biol 2001;134:232-245.
-
(2001)
J Struct Biol
, vol.134
, pp. 232-245
-
-
Di Gennaro, J.A.1
Siew, N.2
Hoffman, B.T.3
Zhang, L.4
Skolnick, J.5
Neilson, L.I.6
Fetrow, J.S.7
-
15
-
-
0035191439
-
Motif-based fold assignment
-
Salwinski L, Eisenberg D. Motif-based fold assignment. Protein Sci 2001;10:2460-2469.
-
(2001)
Protein Sci
, vol.10
, pp. 2460-2469
-
-
Salwinski, L.1
Eisenberg, D.2
-
16
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;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
-
17
-
-
0032169849
-
Protein sequence similarity searches using patterns as seeds
-
Zhang Z, Schaffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res 1998;26:3986-3990.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 3986-3990
-
-
Zhang, Z.1
Schaffer, A.A.2
Miller, W.3
Madden, T.L.4
Lipman, D.J.5
Koonin, E.V.6
Altschul, S.F.7
-
18
-
-
0030777303
-
CATH - A hierarchic classification of protein domain structures
-
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
19
-
-
0032530713
-
CAMPASS: A database of structurally aligned protein superfamilies
-
Sowdhamini R, Burke DF, Huang JF, Mizuguchi K, Nagarajaram HA, Srinivasan N, Steward RE, Blundell TL. CAMPASS: a database of structurally aligned protein superfamilies. Structure 1998;6:1087-1094.
-
(1998)
Structure
, vol.6
, pp. 1087-1094
-
-
Sowdhamini, R.1
Burke, D.F.2
Huang, J.F.3
Mizuguchi, K.4
Nagarajaram, H.A.5
Srinivasan, N.6
Steward, R.E.7
Blundell, T.L.8
-
20
-
-
0031766401
-
HOMSTRAD: A database of protein structure alignments for homologous families
-
Mizuguchi K, Deane CM, Blundell TL, Overington JP. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 1998;7:2469-2471.
-
(1998)
Protein Sci
, vol.7
, pp. 2469-2471
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Overington, J.P.4
-
21
-
-
0032874117
-
Complete genomes in WWW Entrez: Data representation and analysis
-
Tatusova TA, Karsch-Mizrachi I, Ostell JA. Complete genomes in WWW Entrez: data representation and analysis. Bioinformatics 1999;15:536-543.
-
(1999)
Bioinformatics
, vol.15
, pp. 536-543
-
-
Tatusova, T.A.1
Karsch-Mizrachi, I.2
Ostell, J.A.3
-
22
-
-
0027361123
-
A structural basis for sequence comparisons: An evaluation of scoring methodologies
-
Johnson MS, Overington JP. A structural basis for sequence comparisons: an evaluation of scoring methodologies. J Mol Biol 1993;233:716-738.
-
(1993)
J Mol Biol
, vol.233
, pp. 716-738
-
-
Johnson, M.S.1
Overington, J.P.2
-
23
-
-
0028670768
-
Identification of important functional environs in protein tertiary structures from the analysis of residue variation in 3-D: Application to cytochromes c and carboxypeptidases A and B
-
Cardle L, Dufton MJ. Identification of important functional environs in protein tertiary structures from the analysis of residue variation in 3-D: application to cytochromes c and carboxypeptidases A and B. Protein Eng 1994;7:1423-1431.
-
(1994)
Protein Eng
, vol.7
, pp. 1423-1431
-
-
Cardle, L.1
Dufton, M.J.2
-
24
-
-
0022798896
-
Radial locations of amino acid residues in a globular protein: Correlation with the sequence
-
Nishikawa K, Ooi T. Radial locations of amino acid residues in a globular protein: correlation with the sequence. J Biochem (Tokyo) 1986;100:1043-1047.
-
(1986)
J Biochem (Tokyo)
, vol.100
, pp. 1043-1047
-
-
Nishikawa, K.1
Ooi, T.2
-
26
-
-
1542264898
-
PASS2: A semi-automated database of protein alignments organised as structural superfamilies
-
Mallika V, Bhaduri A, Sowdhamini R. PASS2: A semi-automated database of protein alignments organised as structural superfamilies. Nucleic Acids Res 2002;34:252-257.
-
(2002)
Nucleic Acids Res
, vol.34
, pp. 252-257
-
-
Mallika, V.1
Bhaduri, A.2
Sowdhamini, R.3
-
27
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J. Mol Biol 1993;234:779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
28
-
-
0028324332
-
High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR
-
Lodi PJ, Garrett DS, Kuszewski J, Tsang ML, Weatherbee JA, Leonard WJ, Gronenborn AM, Clore GM. High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR. Science 1994;263:1762-1767.
-
(1994)
Science
, vol.263
, pp. 1762-1767
-
-
Lodi, P.J.1
Garrett, D.S.2
Kuszewski, J.3
Tsang, M.L.4
Weatherbee, J.A.5
Leonard, W.J.6
Gronenborn, A.M.7
Clore, G.M.8
-
30
-
-
0029975476
-
Crystal structure of the dual specificity protein phosphatase VHR
-
Yuvaniyama J, Denu JM, Dixon JE, Saper MA. Crystal structure of the dual specificity protein phosphatase VHR. Science 1996;272:1328-1331.
-
(1996)
Science
, vol.272
, pp. 1328-1331
-
-
Yuvaniyama, J.1
Denu, J.M.2
Dixon, J.E.3
Saper, M.A.4
-
31
-
-
0034785827
-
Structural and evolutionary relationships among protein tyrosine phosphatase
-
Andersen JN, Mortensen OH, Peters GH, Drake PG, Iversen LF, Olsen OH, Jansen PG, Andersen HS, Tonks NK, Moller NP. Structural and evolutionary relationships among protein tyrosine phosphatase. Mol Cell Biol 2001;21:7117-7136.
-
(2001)
Mol Cell Biol
, vol.21
, pp. 7117-7136
-
-
Andersen, J.N.1
Mortensen, O.H.2
Peters, G.H.3
Drake, P.G.4
Iversen, L.F.5
Olsen, O.H.6
Jansen, P.G.7
Andersen, H.S.8
Tonks, N.K.9
Moller, N.P.10
-
32
-
-
0036616218
-
The Protein Data Bank
-
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2002;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
Fagan, P.11
Marvin, J.12
Padilla, D.13
Ravichandran, V.14
Schneider, B.15
Thanki, N.16
Weissig, H.17
Westbrook, J.D.18
Zardecki, C.19
-
33
-
-
0036084361
-
The PROSITE database, its status in 2002
-
Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res 2002;30:235-238.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 235-238
-
-
Falquet, L.1
Pagni, M.2
Bucher, P.3
Hulo, N.4
Sigrist, C.J.5
Hofmann, K.6
Bairoch, A.7
-
35
-
-
0029955660
-
An SH3 domain-containing GTPase-activating protein for Rho and Cdc42 associates with focal adhesion kinase
-
Hildebrand JD, Taylor JM, Parsons JT. An SH3 domain-containing GTPase-activating protein for Rho and Cdc42 associates with focal adhesion kinase. Mol Cell Biol 1996;16:3169-3178.
-
(1996)
Mol Cell Biol
, vol.16
, pp. 3169-3178
-
-
Hildebrand, J.D.1
Taylor, J.M.2
Parsons, J.T.3
-
36
-
-
0032521559
-
Interaction of two proline-rich sequences of cell adhesion kinase beta with SH3 domains of p130Cas-related proteins and a GTPase-activating protein
-
Ohba T, Ishino M, Aoto H, Sasaki T. Interaction of two proline-rich sequences of cell adhesion kinase beta with SH3 domains of p130Cas-related proteins and a GTPase-activating protein. Graf Biochem J 1998;330:1249-1254.
-
(1998)
Graf Biochem J
, vol.330
, pp. 1249-1254
-
-
Ohba, T.1
Ishino, M.2
Aoto, H.3
Sasaki, T.4
-
37
-
-
0027176142
-
Refinement of recombinant oncomodulin at 1.30 Å resolution
-
Ahmed FR, Rose DR, Evans SV, Pippy ME, To R. Refinement of recombinant oncomodulin at 1.30 Å resolution. J Mol Biol 1993;230:1216-1224.
-
(1993)
J Mol Biol
, vol.230
, pp. 1216-1224
-
-
Ahmed, F.R.1
Rose, D.R.2
Evans, S.V.3
Pippy, M.E.4
To, R.5
-
38
-
-
0025807187
-
Counting and discounting the universe of exons
-
Doolittle RF. Counting and discounting the universe of exons. Science 1991;253:677-680.
-
(1991)
Science
, vol.253
, pp. 677-680
-
-
Doolittle, R.F.1
-
39
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986;5:823-826.
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
40
-
-
0035254936
-
Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins
-
Reddy BV, Li WW, Shindyalov IN, Bourne PE. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. Proteins 2001;42:148-163.
-
(2001)
Proteins
, vol.42
, pp. 148-163
-
-
Reddy, B.V.1
Li, W.W.2
Shindyalov, I.N.3
Bourne, P.E.4
-
41
-
-
0028246722
-
PRINTS - A protein motif fingerprint database
-
Attwood TK, Beck ME. PRINTS - a protein motif fingerprint database. Protein Eng 1994;7:841-848.
-
(1994)
Protein Eng
, vol.7
, pp. 841-848
-
-
Attwood, T.K.1
Beck, M.E.2
-
42
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli SS, Russell RB. Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol 2000;303:61-76.
-
(2000)
J Mol Biol
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russell, R.B.2
-
43
-
-
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, Blundell TL. 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 1990;212:403-428.
-
(1990)
J Mol Biol
, vol.212
, pp. 403-428
-
-
Sali, A.1
Blundell, T.L.2
-
44
-
-
0025104478
-
Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
-
Overington J, Johnson MS, Sali A, Blundell TL. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc R Soc Lond B Biol Sci 1990;241:132-145.
-
(1990)
Proc R Soc Lond B Biol Sci
, vol.241
, pp. 132-145
-
-
Overington, J.1
Johnson, M.S.2
Sali, A.3
Blundell, T.L.4
-
45
-
-
0031714858
-
JOY: Protein sequence-structure representation and analysis
-
Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP. JOY: protein sequence-structure representation and analysis. Bioinformatics 1998;14:617-623.
-
(1998)
Bioinformatics
, vol.14
, pp. 617-623
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Johnson, M.S.4
Overington, J.P.5
-
46
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
-
(1991)
J Appl Crystallogr
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
47
-
-
0036087630
-
CDD: A database of conserved domain alignments with links to domain three-dimensional structure
-
Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 2002;30:281-283.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 281-283
-
-
Marchler-Bauer, A.1
Panchenko, A.R.2
Shoemaker, B.A.3
Thiessen, P.A.4
Geer, L.Y.5
Bryant, S.H.6
|