-
1
-
-
0000793139
-
Cramming more components onto integrated circuits
-
Moore G. Cramming more components onto integrated circuits. Electronics. 38:1965;114-117.
-
(1965)
Electronics
, vol.38
, pp. 114-117
-
-
Moore, G.1
-
2
-
-
0032521218
-
Marrying structure and genomics
-
Rost B. Marrying structure and genomics. Structure. 6:1998;259-263.
-
(1998)
Structure
, vol.6
, pp. 259-263
-
-
Rost, B.1
-
3
-
-
0012873841
-
Chip "law" expands beyond its creator's wildest expectations
-
Moore G., Dillon P. Chip "law" expands beyond its creator's wildest expectations. Forbes. 25(March):2002;66.
-
(2002)
Forbes
, vol.25
, Issue.MARCH
, pp. 66
-
-
Moore, G.1
Dillon, P.2
-
4
-
-
0036322695
-
Target space for structural genomics revisited
-
Can we cluster sequence-space by grouping full-length proteins? The authors show that single linkage clustering is doomed to fail if proteins cannot be dissected into domains
-
Liu J., Rost B. Target space for structural genomics revisited. Bioinformatics. 18:2002;922-933 Can we cluster sequence-space by grouping full-length proteins? The authors show that single linkage clustering is doomed to fail if proteins cannot be dissected into domains.
-
(2002)
Bioinformatics
, vol.18
, pp. 922-933
-
-
Liu, J.1
Rost, B.2
-
5
-
-
0036601151
-
Did evolution leap to create the protein universe?
-
Rost B. Did evolution leap to create the protein universe? Curr. Opin. Struct. Biol. 12:2002;409-416.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 409-416
-
-
Rost, B.1
-
6
-
-
0036308741
-
Enzyme function less conserved than anticipated
-
Rost B. Enzyme function less conserved than anticipated. J. Mol. Biol. 318:2002;595-608.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 595-608
-
-
Rost, B.1
-
7
-
-
0037249644
-
NLSdb: Database of nuclear localization signals
-
in press
-
Nair R, Carter P, Rost B: NLSdb: database of nuclear localization signals. Nucleic Acids Res 2002, in press.
-
(2002)
Nucleic Acids Res
-
-
Nair, R.1
Carter, P.2
Rost, B.3
-
8
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
Nagano N., Orengo C., Thornton J. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321:2002;741.
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 741
-
-
Nagano, N.1
Orengo, C.2
Thornton, J.3
-
9
-
-
0032944238
-
The PROSITE database, its status in 1999
-
Hofmann K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucleic Acids Res. 27:1999;215-219.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 215-219
-
-
Hofmann, K.1
Bucher, P.2
Falquet, L.3
Bairoch, A.4
-
10
-
-
0001290045
-
PROSITE: A documented database using patterns and profiles as motif descriptors
-
Sigrist C.J., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinf. 3:2002;265-274.
-
(2002)
Brief Bioinf.
, vol.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
Gattiker, A.4
Falquet, L.5
Pagni, M.6
Bairoch, A.7
Bucher, P.8
-
11
-
-
0036084361
-
The PROSITE database, its status in 2002
-
Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res. 30:2002;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
-
12
-
-
0001619859
-
High-quality protein knowledge resource: SWISS-PROT and TrEMBL
-
O'Donovan C., Martin M.J., Gattiker A., Gasteiger E., Bairoch A., Apweiler R. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform. 3:2002;275-284.
-
(2002)
Brief Bioinform.
, vol.3
, pp. 275-284
-
-
O'Donovan, C.1
Martin, M.J.2
Gattiker, A.3
Gasteiger, E.4
Bairoch, A.5
Apweiler, R.6
-
14
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
15
-
-
18444381153
-
PRINTS and PRINTS-S shed light on protein ancestry
-
Attwood T.K., Blythe M.J., Flower D.R., Gaulton A., Mabey J.E., Maudling N., McGregor L., Mitchell A.L., Moulton G., Paine K.et al. PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res. 30:2002;239-241.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 239-241
-
-
Attwood, T.K.1
Blythe, M.J.2
Flower, D.R.3
Gaulton, A.4
Mabey, J.E.5
Maudling, N.6
McGregor, L.7
Mitchell, A.L.8
Moulton, G.9
Paine, K.10
-
16
-
-
0011542799
-
The Pfam protein families database
-
Pfam is by far the most comprehensive manually curated protein family database. High quality is achieved by assuring the incorporation of accurate seed alignments and iterative refinement steps
-
Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 30:2002;276-280 Pfam is by far the most comprehensive manually curated protein family database. High quality is achieved by assuring the incorporation of accurate seed alignments and iterative refinement steps.
-
(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
-
17
-
-
0000120520
-
ProDom: Automated clustering of homologous domains
-
Servant F., Bru C., Carrere S., Courcelle E., Gouzy J., Peyruc D., Kahn D. ProDom: automated clustering of homologous domains. Brief Bioinform. 3:2002;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
-
18
-
-
0032436341
-
DOMO: A new database of aligned protein domains
-
Gracy J., Argos P. DOMO: a new database of aligned protein domains. Trends Biochem. Sci. 23:1998;495-497.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 495-497
-
-
Gracy, J.1
Argos, P.2
-
19
-
-
0036084625
-
SCOP database in 2002: Refinements accommodate structural genomics
-
Lo Conte L., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res. 30:2002;264-267.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 264-267
-
-
Lo Conte, L.1
Brenner, S.E.2
Hubbard, T.J.3
Chothia, C.4
Murzin, A.G.5
-
20
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gillliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gillliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
21
-
-
0036205337
-
The CATH protein family database: A resource for structural and functional annotation of genomes
-
Orengo C.A., Bray J.E., Buchan D.W., Harrison A., Lee D., Pearl F.M., Sillitoe I., Todd A.E., Thornton J.M. The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics. 2:2002;11-21.
-
(2002)
Proteomics
, vol.2
, pp. 11-21
-
-
Orengo, C.A.1
Bray, J.E.2
Buchan, D.W.3
Harrison, A.4
Lee, D.5
Pearl, F.M.6
Sillitoe, I.7
Todd, A.E.8
Thornton, J.M.9
-
22
-
-
0034753838
-
Identification of homology in protein structure classification
-
Dietmann S., Holm L. Identification of homology in protein structure classification. Nat. Struct. Biol. 8:2001;953-957.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 953-957
-
-
Dietmann, S.1
Holm, L.2
-
23
-
-
0037103044
-
Comparison of sequence and structure alignments for protein domains
-
Marchler-Bauer A., Panchenko A.R., Ariel N., Bryant S.H. Comparison of sequence and structure alignments for protein domains. Proteins. 48:2002;439-446.
-
(2002)
Proteins
, vol.48
, pp. 439-446
-
-
Marchler-Bauer, A.1
Panchenko, A.R.2
Ariel, N.3
Bryant, S.H.4
-
24
-
-
0034682894
-
An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence
-
Yang A.S., Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J. Mol. Biol. 301:2000;679-689.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 679-689
-
-
Yang, A.S.1
Honig, B.2
-
25
-
-
0035175673
-
TIGRFAMs: A protein family resource for the functional identification of proteins
-
Haft D.H., Loftus B.J., Richardson D.L., Yang F., Eisen J.A., Paulsen I.T., White O. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29:2001;41-43.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 41-43
-
-
Haft, D.H.1
Loftus, B.J.2
Richardson, D.L.3
Yang, F.4
Eisen, J.A.5
Paulsen, I.T.6
White, O.7
-
26
-
-
0036086410
-
Recent improvements to the SMART domain-based sequence annotation resource
-
Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., Ciccarelli F., Copley R.R., Ponting C.P., Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30:2002;242-244.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 242-244
-
-
Letunic, I.1
Goodstadt, L.2
Dickens, N.J.3
Doerks, T.4
Schultz, J.5
Mott, R.6
Ciccarelli, F.7
Copley, R.R.8
Ponting, C.P.9
Bork, P.10
-
27
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer A.A., Aravind L., Madden T.L., Shavirin S., Spouge J.L., Wolf Y.I., Koonin E.V., Altschul S.F. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29:2001;2994-3005.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
28
-
-
0035998736
-
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh A., Scott A.F., Amberger J., Bocchini C., Valle D., McKusick V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 30:2002;52-55.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 52-55
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.3
Bocchini, C.4
Valle, D.5
McKusick, V.A.6
-
29
-
-
0036083833
-
The SBASE protein domain library, release 9.0: An online resource for protein domain identification
-
Vlahovicek K., Murvai J., Barta E., Pongor S. The SBASE protein domain library, release 9.0: an online resource for protein domain identification. Nucleic Acids Res. 30:2002;273-275.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 273-275
-
-
Vlahovicek, K.1
Murvai, J.2
Barta, E.3
Pongor, S.4
-
30
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., Kiryutin B., Galperin M.Y., Fedorova N.D., Koonin E.V. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:2001;22-28.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
31
-
-
0035166973
-
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
-
InterPro provides a unified documentation resource for protein families, domains and functional sites by merging annotations from several motif/domain databases. All member databases are accessible and searchable through one common, intuitive interface
-
Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D.et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:2001;37-40 InterPro provides a unified documentation resource for protein families, domains and functional sites by merging annotations from several motif/domain databases. All member databases are accessible and searchable through one common, intuitive interface.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 37-40
-
-
Apweiler, R.1
Attwood, T.K.2
Bairoch, A.3
Bateman, A.4
Birney, E.5
Biswas, M.6
Bucher, P.7
Cerutti, L.8
Corpet, F.9
Croning, M.D.10
-
32
-
-
18444400543
-
The Protein Information Resource: An integrated public resource of functional annotation of proteins
-
Wu C.H., Huang H., Arminski L., Castro-Alvear J., Chen Y., Hu Z.Z., Ledley R.S., Lewis K.C., Mewes H.W., Orcutt B.C.et al. The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res. 30:2002;35-37.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 35-37
-
-
Wu, C.H.1
Huang, H.2
Arminski, L.3
Castro-Alvear, J.4
Chen, Y.5
Hu, Z.Z.6
Ledley, R.S.7
Lewis, K.C.8
Mewes, H.W.9
Orcutt, B.C.10
-
33
-
-
0035075436
-
MetaFam: A unified classification of protein families. I. Overview and statistics
-
A unified protein family classification is built automatically on the basis of 10 original databases using set-theory. By combining different resources, proteins are added to families and conflicting annotations are identified
-
Silverstein K.A., Shoop E., Johnson J.E., Retzel E.F. MetaFam: a unified classification of protein families. I. Overview and statistics. Bioinformatics. 17:2001;249-261 A unified protein family classification is built automatically on the basis of 10 original databases using set-theory. By combining different resources, proteins are added to families and conflicting annotations are identified.
-
(2001)
Bioinformatics
, vol.17
, pp. 249-261
-
-
Silverstein, K.A.1
Shoop, E.2
Johnson, J.E.3
Retzel, E.F.4
-
34
-
-
0036330266
-
Selecting targets for structural determination by navigating in a graph of protein families
-
Portugaly E., Kifer I., Linial M. Selecting targets for structural determination by navigating in a graph of protein families. Bioinformatics. 18:2002;899-907.
-
(2002)
Bioinformatics
, vol.18
, pp. 899-907
-
-
Portugaly, E.1
Kifer, I.2
Linial, M.3
-
35
-
-
0036087099
-
SYSTERS, GeneNest, SpliceNest: Exploring sequence space from genome to protein
-
Krause A., Haas S.A., Coward E., Vingron M. SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein. Nucleic Acids Res. 30:2002;299-300.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 299-300
-
-
Krause, A.1
Haas, S.A.2
Coward, E.3
Vingron, M.4
-
36
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B. Twilight zone of protein sequence alignments. Protein Eng. 12:1999;85-94.
-
(1999)
Protein Eng.
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
37
-
-
0036891705
-
Sequence conserved for sub-cellular localization
-
in press
-
Nair R, Rost B: Sequence conserved for sub-cellular localization. Protein Sci 2002, in press.
-
(2002)
Protein Sci
-
-
Nair, R.1
Rost, B.2
-
38
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Thorough overview of the structural backgrounds of enzymatic activity. All 31 enzyme super-families investigated exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a super-family, whilst the reaction chemistry is maintained
-
Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143 Thorough overview of the structural backgrounds of enzymatic activity. All 31 enzyme super-families investigated exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a super-family, whilst the reaction chemistry is maintained.
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
39
-
-
0035424599
-
Intrinsic errors in genome annotation
-
The authors estimate the magnitude of possible annotation errors in automatic transfer of functional classification. They conclude that the number of potential errors in the prediction of detailed functions is higher than is usually believed
-
Devos D., Valencia A. Intrinsic errors in genome annotation. Trends Genet. 17:2001;429-431 The authors estimate the magnitude of possible annotation errors in automatic transfer of functional classification. They conclude that the number of potential errors in the prediction of detailed functions is higher than is usually believed.
-
(2001)
Trends Genet.
, vol.17
, pp. 429-431
-
-
Devos, D.1
Valencia, A.2
-
40
-
-
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., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;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
-
41
-
-
0033944826
-
GeneRAGE: A robust algorithm for sequence clustering and domain detection
-
Enright A.J., Ouzounis C.A. GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics. 16:2000;451-457.
-
(2000)
Bioinformatics
, vol.16
, pp. 451-457
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
42
-
-
0033965852
-
ProtoMap: Automatic classification of protein sequences and hierarchy of protein families
-
Yona G., Linial N., Linial M. ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res. 28:2000;49-55.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 49-55
-
-
Yona, G.1
Linial, N.2
Linial, M.3
-
43
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
A novel method using a Markov Cluster algorithm was used to assign protein sequences into families. Multi-domain proteins are accounted for implicitly. The method is relatively fast
-
Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:2002;1575-1584 A novel method using a Markov Cluster algorithm was used to assign protein sequences into families. Multi-domain proteins are accounted for implicitly. The method is relatively fast.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
44
-
-
0034777598
-
Clustering protein sequences - Structure prediction by transitive homology
-
The authors present a graph-theory-based clustering algorithm. Length-normalised alignment scores are expressed as directed edges in the graph, and clustering is based on the concept of strongly connected components (SCC)
-
Bolten E., Schliep A., Schneckener S., Schomburg D., Schrader R. Clustering protein sequences - structure prediction by transitive homology. Bioinformatics. 17:2001;935-941 The authors present a graph-theory-based clustering algorithm. Length-normalised alignment scores are expressed as directed edges in the graph, and clustering is based on the concept of strongly connected components (SCC).
-
(2001)
Bioinformatics
, vol.17
, pp. 935-941
-
-
Bolten, E.1
Schliep, A.2
Schneckener, S.3
Schomburg, D.4
Schrader, R.5
-
46
-
-
0036307493
-
Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
-
The authors present a novel approach to profile-profile comparisons. The resulting new method appears significantly more sensitive in detecting distant homologies than PSI-BLAST and IMPALA. The resulting method is applied to cluster all protein sequences in BioSphere
-
Yona G., Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol. 315:2002;1257-1275 The authors present a novel approach to profile-profile comparisons. The resulting new method appears significantly more sensitive in detecting distant homologies than PSI-BLAST and IMPALA. The resulting method is applied to cluster all protein sequences in BioSphere.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 1257-1275
-
-
Yona, G.1
Levitt, M.2
-
47
-
-
0001899680
-
The metric space of proteins-comparative study of clustering algorithms
-
ProtoNet provides a hierarchical view of the protein universe. It starts with many small clusters with very high similarity, and merges and clusters at different similarity levels. Different merging rules and termination rules are explored and compared to achieve optimal results
-
Sasson O., Linial N., Linial M. The metric space of proteins-comparative study of clustering algorithms. Bioinformatics. 18(Suppl. 1):2002;S14-S21 ProtoNet provides a hierarchical view of the protein universe. It starts with many small clusters with very high similarity, and merges and clusters at different similarity levels. Different merging rules and termination rules are explored and compared to achieve optimal results.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Sasson, O.1
Linial, N.2
Linial, M.3
-
48
-
-
0036721254
-
Protein domain identification and improved sequence similarity searching using PSI-BLAST
-
DOMAINATION delineates structural domain-like fragments through analyzing iterative PSI-BLAST alignments. The overall accuracy is estimated to be around 50% for a set of 453 multi-domain proteins
-
George R.A., Heringa J. Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins. 48:2002;672-681 DOMAINATION delineates structural domain-like fragments through analyzing iterative PSI-BLAST alignments. The overall accuracy is estimated to be around 50% for a set of 453 multi-domain proteins.
-
(2002)
Proteins
, vol.48
, pp. 672-681
-
-
George, R.A.1
Heringa, J.2
-
49
-
-
84888070567
-
Protein structural domain parsing by consensus reasoning over multiple knowledge sources and methods
-
Kulikowski C.A., Muchnik I., Yun H.J., Dayanik A.A., Zhang D., Song Y., Montelione G.T. Protein structural domain parsing by consensus reasoning over multiple knowledge sources and methods. Medinfo. 10:2001;965-969.
-
(2001)
Medinfo
, vol.10
, pp. 965-969
-
-
Kulikowski, C.A.1
Muchnik, I.2
Yun, H.J.3
Dayanik, A.A.4
Zhang, D.5
Song, Y.6
Montelione, G.T.7
-
50
-
-
0036306348
-
SnapDRAGON: A method to delineate protein structural domains from sequence data
-
George R.A., Heringa J. SnapDRAGON: a method to delineate protein structural domains from sequence data. J. Mol. Biol. 316:2002;839-851.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 839-851
-
-
George, R.A.1
Heringa, J.2
-
52
-
-
0036288851
-
Characterization and prediction of linker sequences of multi-domain proteins by a neural network
-
Miyazaki S., Kuroda Y., Yokoyama S. Characterization and prediction of linker sequences of multi-domain proteins by a neural network. J. Struct. Funct. Genom. 2:2002;37-51.
-
(2002)
J. Struct. Funct. Genom.
, vol.2
, pp. 37-51
-
-
Miyazaki, S.1
Kuroda, Y.2
Yokoyama, S.3
-
53
-
-
0034887296
-
Prediction of protein functional domains from sequences using artificial neural networks
-
Murvai J., Vlahovicek K., Szepesvari C., Pongor S. Prediction of protein functional domains from sequences using artificial neural networks. Genome Res. 11:2001;1410-1417.
-
(2001)
Genome Res.
, vol.11
, pp. 1410-1417
-
-
Murvai, J.1
Vlahovicek, K.2
Szepesvari, C.3
Pongor, S.4
-
54
-
-
0035022941
-
Intrinsically disordered protein
-
Dunker A.K., Lawson J.D., Brown C.J., Williams R.M., Romero P., Oh J.S., Oldfield C.J., Campen A.M., Ratliff C.M., Hipps K.W.et al. Intrinsically disordered protein. J. Mol. Graph Model. 19:2001;26-59.
-
(2001)
J. Mol. Graph Model
, vol.19
, pp. 26-59
-
-
Dunker, A.K.1
Lawson, J.D.2
Brown, C.J.3
Williams, R.M.4
Romero, P.5
Oh, J.S.6
Oldfield, C.J.7
Campen, A.M.8
Ratliff, C.M.9
Hipps, K.W.10
-
55
-
-
0036968309
-
Loopy proteins appear conserved in evolution
-
Long regions with no regular secondary structure (NORS) are abundant in 30 entirely sequenced organisms, particularly in eukaryotes. These regions are evolutionary conserved, and active in protein-protein interactions. They may constitute candidates for structural domains
-
Liu J., Tan H., Rost B. Loopy proteins appear conserved in evolution. J. Mol. Biol. 322:2002;53-64 Long regions with no regular secondary structure (NORS) are abundant in 30 entirely sequenced organisms, particularly in eukaryotes. These regions are evolutionary conserved, and active in protein-protein interactions. They may constitute candidates for structural domains.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 53-64
-
-
Liu, J.1
Tan, H.2
Rost, B.3
-
57
-
-
0035070578
-
Picasso: Generating a covering set of protein family profiles
-
Picasso clusters the protein universe starting with all-against-all BLAST alignments. The BLAST alignments are then merged on the basis of profile-profile comparison and set theoretic concepts. Structural domain-like fragments are identified from the final multiple alignments
-
Heger A., Holm L. Picasso: generating a covering set of protein family profiles. Bioinformatics. 17:2001;272-279 Picasso clusters the protein universe starting with all-against-all BLAST alignments. The BLAST alignments are then merged on the basis of profile-profile comparison and set theoretic concepts. Structural domain-like fragments are identified from the final multiple alignments.
-
(2001)
Bioinformatics
, vol.17
, pp. 272-279
-
-
Heger, A.1
Holm, L.2
-
58
-
-
0036327988
-
Clustering of proximal sequence space for the identification of protein families
-
The authors propose a clustering strategy derived from minimum cut algorithm in graph theory. Application of the method to a COG dataset gives a similar result to COG classification itself
-
Abascal F., Valencia A. Clustering of proximal sequence space for the identification of protein families. Bioinformatics. 18:2002;908-921 The authors propose a clustering strategy derived from minimum cut algorithm in graph theory. Application of the method to a COG dataset gives a similar result to COG classification itself.
-
(2002)
Bioinformatics
, vol.18
, pp. 908-921
-
-
Abascal, F.1
Valencia, A.2
-
59
-
-
0000515372
-
InterPro: An integrated documentation resource for protein families, domains and functional sites
-
Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Biswas M., Bradley P., Bork P., Bucher P.et al. InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform. 3:2002;225-235.
-
(2002)
Brief Bioinform.
, vol.3
, pp. 225-235
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Biswas, M.7
Bradley, P.8
Bork, P.9
Bucher, P.10
-
61
-
-
0035923596
-
Structural genomics: An approach to the protein folding problem
-
Montelione G.T. Structural genomics: an approach to the protein folding problem. Proc. Natl. Acad. Sci. U.S.A. 98:2001;13488-13489.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 13488-13489
-
-
Montelione, G.T.1
-
62
-
-
18244372730
-
Structural genomics and signaling domains
-
Hurley J.H., Anderson D.E., Beach B., Canagarajah B., Ho Y.S., Jones E., Miller G., Misra S., Pearson M., Saidi L.et al. Structural genomics and signaling domains. Trends Biochem. Sci. 27:2002;48-53.
-
(2002)
Trends Biochem. Sci.
, vol.27
, pp. 48-53
-
-
Hurley, J.H.1
Anderson, D.E.2
Beach, B.3
Canagarajah, B.4
Ho, Y.S.5
Jones, E.6
Miller, G.7
Misra, S.8
Pearson, M.9
Saidi, L.10
-
63
-
-
0036228236
-
Knowledge-based selection of targets for structural genomics
-
Frishman D. Knowledge-based selection of targets for structural genomics. Protein Eng. 15:2002;169-183.
-
(2002)
Protein Eng.
, vol.15
, pp. 169-183
-
-
Frishman, D.1
-
64
-
-
0035783055
-
On the evolution of protein folds: Are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?
-
Lupas A.N., Ponting C.P., Russell R.B. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J. Struct. Biol. 134:2001;191-203.
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 191-203
-
-
Lupas, A.N.1
Ponting, C.P.2
Russell, R.B.3
|