-
1
-
-
0015597839
-
Nucleation, rapid folding, and globular intrachain regions in proteins
-
10.1073/pnas.70.3.697, 433338, 4351801
-
Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 1973, 70:697-701. 10.1073/pnas.70.3.697, 433338, 4351801.
-
(1973)
Proc Natl Acad Sci USA
, vol.70
, pp. 697-701
-
-
Wetlaufer, D.B.1
-
2
-
-
0036089339
-
The natural history of protein domains
-
10.1146/annurev.biophys.31.082901.134314, 11988462
-
Ponting CP, Russell RR. The natural history of protein domains. Annu Rev Biophys Biomol Struct 2002, 31:45-71. 10.1146/annurev.biophys.31.082901.134314, 11988462.
-
(2002)
Annu Rev Biophys Biomol Struct
, vol.31
, pp. 45-71
-
-
Ponting, C.P.1
Russell, R.R.2
-
3
-
-
3543148406
-
Expression screening, protein purification and NMR analysis of human protein domains for structural genomics
-
10.1023/B:JSFG.0000029200.66197.0c, 15263851
-
Folkers GE, van Buuren BN, Kaptein R. Expression screening, protein purification and NMR analysis of human protein domains for structural genomics. J Struct Funct Genomics 2004, 5:119-131. 10.1023/B:JSFG.0000029200.66197.0c, 15263851.
-
(2004)
J Struct Funct Genomics
, vol.5
, pp. 119-131
-
-
Folkers, G.E.1
van Buuren, B.N.2
Kaptein, R.3
-
4
-
-
33645518215
-
Computer-aided NMR assay for detecting natively folded structural domains
-
10.1110/ps.051880406, 2242495, 16522794
-
Hondoh T, Kato A, Yokoyama S, Kuroda Y. Computer-aided NMR assay for detecting natively folded structural domains. Protein Sci 2006, 15:871-883. 10.1110/ps.051880406, 2242495, 16522794.
-
(2006)
Protein Sci
, vol.15
, pp. 871-883
-
-
Hondoh, T.1
Kato, A.2
Yokoyama, S.3
Kuroda, Y.4
-
5
-
-
30344438515
-
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM
-
10.1002/prot.20737, 16187362
-
Kim DE, Chivian D, Malmstrom L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins 2005, 61(Suppl 7):193-200. 10.1002/prot.20737, 16187362.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 193-200
-
-
Kim, D.E.1
Chivian, D.2
Malmstrom, L.3
Baker, D.4
-
6
-
-
36749014942
-
Assessment of predictions submitted for the CASP7 domain prediction category
-
10.1002/prot.21675, 17680686
-
Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins 2007, 69(Suppl 8):137-151. 10.1002/prot.21675, 17680686.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 137-151
-
-
Tress, M.1
Cheng, J.2
Baldi, P.3
Joo, K.4
Lee, J.5
Seo, J.H.6
Baker, D.7
Chivian, D.8
Kim, D.9
Ezkurdia, I.10
-
7
-
-
0033944826
-
GeneRAGE: a robust algorithm for sequence clustering and domain detection
-
10.1093/bioinformatics/16.5.451, 10871267
-
Enright AJ, Ouzounis CA. GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics 2000, 16:451-457. 10.1093/bioinformatics/16.5.451, 10871267.
-
(2000)
Bioinformatics
, vol.16
, pp. 451-457
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
8
-
-
0036721254
-
Protein domain identification and improved sequence similarity searching using PSI-BLAST
-
10.1002/prot.10175, 12211035
-
George RA, Heringa J. Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins 2002, 48:672-681. 10.1002/prot.10175, 12211035.
-
(2002)
Proteins
, vol.48
, pp. 672-681
-
-
George, R.A.1
Heringa, J.2
-
9
-
-
0036306348
-
SnapDRAGON: a method to delineate protein structural domains from sequence data
-
10.1006/jmbi.2001.5387, 11866536
-
George RA, Heringa J. SnapDRAGON: a method to delineate protein structural domains from sequence data. J Mol Biol 2002, 316:839-851. 10.1006/jmbi.2001.5387, 11866536.
-
(2002)
J Mol Biol
, vol.316
, pp. 839-851
-
-
George, R.A.1
Heringa, J.2
-
10
-
-
33747836566
-
KemaDom: a web server for domain prediction using kernel machine with local context
-
10.1093/nar/gkl331, 1538912, 16844982
-
Chen L, Wang W, Ling S, Jia C, Wang F. KemaDom: a web server for domain prediction using kernel machine with local context. Nucleic Acids Res 2006, 34:W158-163. 10.1093/nar/gkl331, 1538912, 16844982.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Chen, L.1
Wang, W.2
Ling, S.3
Jia, C.4
Wang, F.5
-
11
-
-
33745101459
-
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks
-
Cheng J, Sweredoski M, Baldi P. DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. Data Mining and Knowledge Discovery 2006, 13:1-10.
-
(2006)
Data Mining and Knowledge Discovery
, vol.13
, pp. 1-10
-
-
Cheng, J.1
Sweredoski, M.2
Baldi, P.3
-
12
-
-
3142680264
-
Automatic prediction of protein domains from sequence information using a hybrid learning system
-
10.1093/bioinformatics/bth086, 14962932
-
Nagarajan N, Yona G. Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics 2004, 20:1335-1360. 10.1093/bioinformatics/bth086, 14962932.
-
(2004)
Bioinformatics
, vol.20
, pp. 1335-1360
-
-
Nagarajan, N.1
Yona, G.2
-
13
-
-
17844363963
-
PPRODO: prediction of protein domain boundaries using neural networks
-
10.1002/prot.20442, 15789433
-
Sim J, Kim SY, Lee J. PPRODO: prediction of protein domain boundaries using neural networks. Proteins 2005, 59:627-632. 10.1002/prot.20442, 15789433.
-
(2005)
Proteins
, vol.59
, pp. 627-632
-
-
Sim, J.1
Kim, S.Y.2
Lee, J.3
-
14
-
-
58149336791
-
Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries
-
OPUS-Dom
-
Wu Y, Dousis AD, Chen M, Li J, Ma J, . OPUS-Dom Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries. J Mol Boil 2009, 385:1314-1329. OPUS-Dom.
-
(2009)
J Mol Boil
, vol.385
, pp. 1314-1329
-
-
Wu, Y.1
Dousis, A.D.2
Chen, M.3
Li, J.4
Ma, J.5
-
15
-
-
67650898274
-
Ab initio and homology based prediction of protein domains by recursive neural networks
-
10.1186/1471-2105-10-195, 2711945, 19558651
-
Walsh I, Martin AJ, Mooney C, Rubagotti E, Vullo A, Pollastri G. Ab initio and homology based prediction of protein domains by recursive neural networks. BMC Bioinformatics 2009, 10:195. 10.1186/1471-2105-10-195, 2711945, 19558651.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 195
-
-
Walsh, I.1
Martin, A.J.2
Mooney, C.3
Rubagotti, E.4
Vullo, A.5
Pollastri, G.6
-
16
-
-
34547591340
-
DOMAC: an accurate, hybrid protein domain prediction server
-
10.1093/nar/gkm390, 1933197, 17553833
-
Cheng J. DOMAC: an accurate, hybrid protein domain prediction server. Nucleic Acids Res 2007, 35:W354-356. 10.1093/nar/gkm390, 1933197, 17553833.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Cheng, J.1
-
17
-
-
3042810008
-
Sequence-based prediction of protein domains
-
10.1093/nar/gkh684, 484172, 15240828
-
Liu J, Rost B. Sequence-based prediction of protein domains. Nucleic Acids Res 2004, 32:3522-3530. 10.1093/nar/gkh684, 484172, 15240828.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3522-3530
-
-
Liu, J.1
Rost, B.2
-
18
-
-
0033753811
-
Domain size distributions can predict domain boundaries
-
10.1093/bioinformatics/16.7.613, 11038331
-
Wheelan SJ, Marchler-Bauer A, Bryant SH. Domain size distributions can predict domain boundaries. Bioinformatics 2000, 16:613-618. 10.1093/bioinformatics/16.7.613, 11038331.
-
(2000)
Bioinformatics
, vol.16
, pp. 613-618
-
-
Wheelan, S.J.1
Marchler-Bauer, A.2
Bryant, S.H.3
-
19
-
-
0028276887
-
A workbench for large-scale sequence homology analysis
-
Sonnhammer EL, Durbin R. A workbench for large-scale sequence homology analysis. Comput Appl Biosci 1994, 10:301-307.
-
(1994)
Comput Appl Biosci
, vol.10
, pp. 301-307
-
-
Sonnhammer, E.L.1
Durbin, R.2
-
20
-
-
0033563522
-
Whole genome protein domain analysis using a new method for domain clustering
-
10.1016/S0097-8485(99)00011-X, 10404623
-
Gouzy J, Corpet F, Kahn D. Whole genome protein domain analysis using a new method for domain clustering. Comput Chem 1999, 23:333-340. 10.1016/S0097-8485(99)00011-X, 10404623.
-
(1999)
Comput Chem
, vol.23
, pp. 333-340
-
-
Gouzy, J.1
Corpet, F.2
Kahn, D.3
-
21
-
-
0031857779
-
Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similarities
-
10.1093/bioinformatics/14.2.174, 9545450
-
Gracy J, Argos P. Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similarities. Bioinformatics 1998, 14:174-187. 10.1093/bioinformatics/14.2.174, 9545450.
-
(1998)
Bioinformatics
, vol.14
, pp. 174-187
-
-
Gracy, J.1
Argos, P.2
-
22
-
-
0034493084
-
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics
-
10.1110/ps.9.12.2313, 2144534, 11206052
-
Kuroda Y, Tani K, Matsuo Y, Yokoyama S. Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. Protein Sci 2000, 9:2313-2321. 10.1110/ps.9.12.2313, 2144534, 11206052.
-
(2000)
Protein Sci
, vol.9
, pp. 2313-2321
-
-
Kuroda, Y.1
Tani, K.2
Matsuo, Y.3
Yokoyama, S.4
-
23
-
-
0030003048
-
Multiple domain protein diagnostic patterns
-
10.1002/pro.5560050703, 2143450, 8819157
-
Adams RM, Das S, Smith TF. Multiple domain protein diagnostic patterns. Protein Sci 1996, 5:1240-1249. 10.1002/pro.5560050703, 2143450, 8819157.
-
(1996)
Protein Sci
, vol.5
, pp. 1240-1249
-
-
Adams, R.M.1
Das, S.2
Smith, T.F.3
-
24
-
-
0031874788
-
DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins
-
10.1093/bioinformatics/14.2.144, 9545446
-
Park J, Teichmann SA. DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics 1998, 14:144-150. 10.1093/bioinformatics/14.2.144, 9545446.
-
(1998)
Bioinformatics
, vol.14
, pp. 144-150
-
-
Park, J.1
Teichmann, S.A.2
-
25
-
-
0042622240
-
GlobPlot: Exploring protein sequences for globularity and disorder
-
10.1093/nar/gkg519, 169197, 12824398
-
Linding R, Russell RB, Neduva V, Gibson TJ. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 2003, 31:3701-3708. 10.1093/nar/gkg519, 169197, 12824398.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3701-3708
-
-
Linding, R.1
Russell, R.B.2
Neduva, V.3
Gibson, T.J.4
-
26
-
-
0033982651
-
Role of linkers in communication between protein modules
-
10.1016/S1367-5931(99)00046-0, 10679375
-
Gokhale RS, Khosla C. Role of linkers in communication between protein modules. Curr Opin Chem Biol 2000, 4:22-27. 10.1016/S1367-5931(99)00046-0, 10679375.
-
(2000)
Curr Opin Chem Biol
, vol.4
, pp. 22-27
-
-
Gokhale, R.S.1
Khosla, C.2
-
27
-
-
33645741221
-
Improvement of domain linker prediction by incorporating loop-length-dependent characteristics
-
Tanaka T, Yokoyama S, Kuroda Y. Improvement of domain linker prediction by incorporating loop-length-dependent characteristics. Peptide Science 2006, 84:161-168.
-
(2006)
Peptide Science
, vol.84
, pp. 161-168
-
-
Tanaka, T.1
Yokoyama, S.2
Kuroda, Y.3
-
28
-
-
0036878154
-
An analysis of protein domain linkers: their classification and role in protein folding
-
10.1093/protein/15.11.871, 12538906
-
George RA, Heringa J. An analysis of protein domain linkers: their classification and role in protein folding. Protein Engineering 2002, 15:871-879. 10.1093/protein/15.11.871, 12538906.
-
(2002)
Protein Engineering
, vol.15
, pp. 871-879
-
-
George, R.A.1
Heringa, J.2
-
29
-
-
0030777303
-
CATH--a hierarchic classification of protein domain structures
-
10.1016/S0969-2126(97)00260-8, 9309224
-
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. 10.1016/S0969-2126(97)00260-8, 9309224.
-
(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
-
30
-
-
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
-
31
-
-
0032189646
-
Dictionary of recurrent domains in protein structures
-
10.1002/(SICI)1097-0134(19981001)33:1<88::AID-PROT8>3.0.CO;2-H, 9741847
-
Holm L, Sander C. Dictionary of recurrent domains in protein structures. Proteins 1998, 33:88-96. 10.1002/(SICI)1097-0134(19981001)33:1<88::AID-PROT8>3.0.CO;2-H, 9741847.
-
(1998)
Proteins
, vol.33
, pp. 88-96
-
-
Holm, L.1
Sander, C.2
-
32
-
-
0031865006
-
Touring protein fold space with Dali/FSSP
-
10.1093/nar/26.1.316, 147193, 9399863
-
Holm L, Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res 1998, 26:316-319. 10.1093/nar/26.1.316, 147193, 9399863.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 316-319
-
-
Holm, L.1
Sander, C.2
-
33
-
-
13144259695
-
Relative rates of gene fusion and fission in multi-domain proteins
-
10.1016/j.tig.2004.11.007, 15680510
-
Kummerfeld SK, Teichmann SA. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet 2005, 21:25-30. 10.1016/j.tig.2004.11.007, 15680510.
-
(2005)
Trends Genet
, vol.21
, pp. 25-30
-
-
Kummerfeld, S.K.1
Teichmann, S.A.2
-
34
-
-
33745611416
-
Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
-
10.1093/bioinformatics/btl135, 16601004
-
Pasek S, Risler JL, Brezellec P. Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins. Bioinformatics 2006, 22:1418-1423. 10.1093/bioinformatics/btl135, 16601004.
-
(2006)
Bioinformatics
, vol.22
, pp. 1418-1423
-
-
Pasek, S.1
Risler, J.L.2
Brezellec, P.3
-
35
-
-
0025900486
-
Shuffled domains in extracellular proteins
-
10.1016/0014-5793(91)80937-X, 1864378
-
Bork P. Shuffled domains in extracellular proteins. FEBS Lett 1991, 286:47-54. 10.1016/0014-5793(91)80937-X, 1864378.
-
(1991)
FEBS Lett
, vol.286
, pp. 47-54
-
-
Bork, P.1
-
36
-
-
0029006062
-
The multiplicity of domains in proteins
-
10.1146/annurev.bi.64.070195.001443, 7574483
-
Doolittle RF. The multiplicity of domains in proteins. Annu Rev Biochem 1995, 64:287-314. 10.1146/annurev.bi.64.070195.001443, 7574483.
-
(1995)
Annu Rev Biochem
, vol.64
, pp. 287-314
-
-
Doolittle, R.F.1
-
37
-
-
0030989408
-
Three-dimensional domain duplication, swapping and stealing
-
10.1016/S0959-440X(97)80060-7, 9204285
-
Heringa J, Taylor WR. Three-dimensional domain duplication, swapping and stealing. Curr Opin Struct Biol 1997, 7:416-421. 10.1016/S0959-440X(97)80060-7, 9204285.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 416-421
-
-
Heringa, J.1
Taylor, W.R.2
-
38
-
-
0028865843
-
3D domain swapping: a mechanism for oligomer assembly
-
10.1002/pro.5560041202, 2143041, 8580836
-
Bennett MJ, Schlunegger MP, Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci 1995, 4:2455-2468. 10.1002/pro.5560041202, 2143041, 8580836.
-
(1995)
Protein Sci
, vol.4
, pp. 2455-2468
-
-
Bennett, M.J.1
Schlunegger, M.P.2
Eisenberg, D.3
-
39
-
-
9144257886
-
The Pfam protein families database
-
10.1093/nar/gkh121, 308855, 14681378
-
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al. The Pfam protein families database. Nucleic Acids Res 2004, 32:D138-141. 10.1093/nar/gkh121, 308855, 14681378.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.10
-
40
-
-
0027564279
-
The evolutionary history of the first three enzymes in pyrimidine biosynthesis
-
10.1002/bies.950150303, 8098212
-
Davidson JN, Chen KC, Jamison RS, Musmanno LA, Kern CB. The evolutionary history of the first three enzymes in pyrimidine biosynthesis. Bioessays 1993, 15:157-164. 10.1002/bies.950150303, 8098212.
-
(1993)
Bioessays
, vol.15
, pp. 157-164
-
-
Davidson, J.N.1
Chen, K.C.2
Jamison, R.S.3
Musmanno, L.A.4
Kern, C.B.5
-
41
-
-
62949185014
-
Bioinformatics and Genomes: Current Perspectives
-
Heidelberg, Germany: Horizon Scientific Press, (Ed.)
-
Andrade, . (Ed.) Bioinformatics and Genomes: Current Perspectives. 2003, Heidelberg, Germany: Horizon Scientific Press, (Ed.).
-
(2003)
-
-
Andrade1
-
42
-
-
0037251892
-
NCBI Reference Sequence project: update and current status
-
10.1093/nar/gkg111, 165558, 12519942
-
Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence project: update and current status. Nucleic Acids Res 2003, 31:34-37. 10.1093/nar/gkg111, 165558, 12519942.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 34-37
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
43
-
-
84888283542
-
PDB identifiers and domain definitions
-
PDB identifiers and domain definitions. , http://casp.rnet.missouri.edu/download/
-
-
-
-
44
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
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. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(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
-
45
-
-
0036893072
-
Rapid protein domain assignment from amino acid sequence using predicted secondary structure
-
10.1110/ps.0209902, 2373756, 12441380
-
Marsden RL, McGuffin LJ, Jones DT. Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci 2002, 11:2814-2824. 10.1110/ps.0209902, 2373756, 12441380.
-
(2002)
Protein Sci
, vol.11
, pp. 2814-2824
-
-
Marsden, R.L.1
McGuffin, L.J.2
Jones, D.T.3
-
47
-
-
0002714543
-
Making large-scale support vector machine learning practical
-
MIT Press
-
Joachims T. Making large-scale support vector machine learning practical. Advances in kernel methods: support vector learning 1999, 169-184. MIT Press.
-
(1999)
Advances in kernel methods: support vector learning
, pp. 169-184
-
-
Joachims, T.1
-
48
-
-
23144465987
-
SCRATCH: a protein structure and structural feature prediction server
-
10.1093/nar/gki396, 1160157, 15980571
-
Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 2005, 33:W72-76. 10.1093/nar/gki396, 1160157, 15980571.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Cheng, J.1
Randall, A.Z.2
Sweredoski, M.J.3
Baldi, P.4
-
49
-
-
84888285026
-
CASP9
-
CASP9. , http://www.predictioncenter.org/casp9/index.cgi
-
-
-
|