-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F. et al. (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
-
2
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann,B. 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
-
3
-
-
33947190606
-
T cell immunoglobulin mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface
-
Cao,E. et al. (2007) T cell immunoglobulin mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface. Immunity, 26, 311-321.
-
(2007)
Immunity
, vol.26
, pp. 311-321
-
-
Cao, E.1
-
4
-
-
33646172143
-
Structural classification of small, disulfide-rich protein domains
-
Cheek,S. et al. (2006) Structural classification of small, disulfide-rich protein domains. J. Mol. Biol., 359, 215-237.
-
(2006)
J. Mol. Biol
, vol.359
, pp. 215-237
-
-
Cheek, S.1
-
5
-
-
27544440502
-
Prediction of disulfide connectivity from protein sequences
-
Chen,Y.C. and Hwang,J.K. (2005) Prediction of disulfide connectivity from protein sequences. Proteins, 61, 507-512.
-
(2005)
Proteins
, vol.61
, pp. 507-512
-
-
Chen, Y.C.1
Hwang, J.K.2
-
6
-
-
2542586190
-
Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences
-
Chen,Y.C. et al. (2004) Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences. Proteins, 55, 1036-1042.
-
(2004)
Proteins
, vol.55
, pp. 1036-1042
-
-
Chen, Y.C.1
-
7
-
-
31944444347
-
Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching
-
Cheng,J. et al. (2006) Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins, 62, 617-629.
-
(2006)
Proteins
, vol.62
, pp. 617-629
-
-
Cheng, J.1
-
8
-
-
33744801136
-
Disulfide connectivity prediction with 70% accuracy using two-level models
-
Chen,B.J. et al. (2006) Disulfide connectivity prediction with 70% accuracy using two-level models. Proteins, 64, 246-252.
-
(2006)
Proteins
, vol.64
, pp. 246-252
-
-
Chen, B.J.1
-
9
-
-
0041819762
-
Relationship between protein structures and disulfide-bonding patterns
-
Chuang,C.C. et al. (2003) Relationship between protein structures and disulfide-bonding patterns. Proteins, 53, 1-5.
-
(2003)
Proteins
, vol.53
, pp. 1-5
-
-
Chuang, C.C.1
-
10
-
-
3543089710
-
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
-
Dekker,J.P. et al. (2004) A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics, 20, 1565-1572.
-
(2004)
Bioinformatics
, vol.20
, pp. 1565-1572
-
-
Dekker, J.P.1
-
11
-
-
0034781580
-
Prediction of disulfide connectivity in proteins
-
Fariselli,P. and Casadio,R. (2001) Prediction of disulfide connectivity in proteins. Bioinformatics, 17, 957-964.
-
(2001)
Bioinformatics
, vol.17
, pp. 957-964
-
-
Fariselli, P.1
Casadio, R.2
-
12
-
-
1842492440
-
A neural network based method for predicting the disulfide connectivity in proteins
-
Damiani,E, ed, IOS Press, Amsterdam, pp
-
Fariselli,P. et al. (2002) A neural network based method for predicting the disulfide connectivity in proteins. In Damiani,E. (ed.) Knowledge Based Intelligent Information Engineering Systems and Allied Technologies (KES). IOS Press, Amsterdam, pp. 464-68.
-
(2002)
Knowledge Based Intelligent Information Engineering Systems and Allied Technologies (KES)
, pp. 464-468
-
-
Fariselli, P.1
-
13
-
-
19544393195
-
Disulfide connectivity prediction using secondary structure information and diresidue frequencies
-
Ferre,F. and Clote,P. (2005) Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinformatics, 21, 2336-2346.
-
(2005)
Bioinformatics
, vol.21
, pp. 2336-2346
-
-
Ferre, F.1
Clote, P.2
-
14
-
-
0026579140
-
Different sequence environments of cysteines and half cystines in proteins. Application to predict disulfide forming residues
-
Fiser,A. et al. (1992) Different sequence environments of cysteines and half cystines in proteins. Application to predict disulfide forming residues. FEBS Lett., 302, 117-120.
-
(1992)
FEBS Lett
, vol.302
, pp. 117-120
-
-
Fiser, A.1
-
15
-
-
0034039497
-
Predicting the oxidation state of cysteines by multiple sequence alignment
-
Fiser,A. and Simon,I. (2000) Predicting the oxidation state of cysteines by multiple sequence alignment. Bioinformatics, 16, 251-256.
-
(2000)
Bioinformatics
, vol.16
, pp. 251-256
-
-
Fiser, A.1
Simon, I.2
-
16
-
-
0036285587
-
Predicting redox state of cysteines in proteins
-
Fiser,A. and Simon,I. (2002) Predicting redox state of cysteines in proteins. Methods Enzymol., 353, 10-21.
-
(2002)
Methods Enzymol
, vol.353
, pp. 10-21
-
-
Fiser, A.1
Simon, I.2
-
17
-
-
0016943409
-
An efficient implementation of edmund's algorithm for maximum weight mathing on graph
-
Gabow,H.N. (1976) An efficient implementation of edmund's algorithm for maximum weight mathing on graph. J. ACM, 23, 221-234.
-
(1976)
J. ACM
, vol.23
, pp. 221-234
-
-
Gabow, H.N.1
-
18
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Gobel,U. et al. (1994) Correlated mutations and residue contacts in proteins. Proteins, 18, 309-317.
-
(1994)
Proteins
, vol.18
, pp. 309-317
-
-
Gobel, U.1
-
19
-
-
3342972674
-
A classification of disulfide patterns and its relationship to protein structure and function
-
Gupta,A. et al. (2004) A classification of disulfide patterns and its relationship to protein structure and function. Protein Sci., 13, 2045-2058.
-
(2004)
Protein Sci
, vol.13
, pp. 2045-2058
-
-
Gupta, A.1
-
20
-
-
4043170491
-
Protein contact prediction using patterns of correlation
-
Hamilton,N. et al. (2004) Protein contact prediction using patterns of correlation. Proteins, 56, 679-684.
-
(2004)
Proteins
, vol.56
, pp. 679-684
-
-
Hamilton, N.1
-
21
-
-
0028063090
-
Analysis and classification of disulphide connectivity in proteins. The entropic effect of cross-linkage
-
Harrison,P.M. and Sternberg,M.J. (1994) Analysis and classification of disulphide connectivity in proteins. The entropic effect of cross-linkage. J. Mol. Biol., 244, 448-463.
-
(1994)
J. Mol. Biol
, vol.244
, pp. 448-463
-
-
Harrison, P.M.1
Sternberg, M.J.2
-
22
-
-
0037397499
-
Disulfide bonds as switches for protein function
-
Hogg,P.J. (2003) Disulfide bonds as switches for protein function. Trends Biochem. Sci., 28, 210-214.
-
(2003)
Trends Biochem. Sci
, vol.28
, pp. 210-214
-
-
Hogg, P.J.1
-
23
-
-
0042768090
-
Protein disulfide bond formation in prokaryotes
-
Kadokura,H. et al. (2003) Protein disulfide bond formation in prokaryotes. Annu. Rev. Biochem., 72, 111-135.
-
(2003)
Annu. Rev. Biochem
, vol.72
, pp. 111-135
-
-
Kadokura, H.1
-
24
-
-
33746218852
-
MUSTANG: A multiple structural alignment algorithm
-
Konagurthu,A.S. et al. (2006) MUSTANG: A multiple structural alignment algorithm. Proteins, 64, 559-574.
-
(2006)
Proteins
, vol.64
, pp. 559-574
-
-
Konagurthu, A.S.1
-
25
-
-
0028826172
-
Paired natural cysteine mutation mapping: Aid to constraining models of protein tertiary structure
-
Kreisberg,R. et al. (1995) Paired natural cysteine mutation mapping: Aid to constraining models of protein tertiary structure. Protein Sci., 4, 2405-2410.
-
(1995)
Protein Sci
, vol.4
, pp. 2405-2410
-
-
Kreisberg, R.1
-
26
-
-
0034721944
-
Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
-
Larson,S.M. et al. (2000) Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol. 303, 433-446.
-
(2000)
J. Mol. Biol
, vol.303
, pp. 433-446
-
-
Larson, S.M.1
-
27
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li,W. and Godzik,A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
28
-
-
33947429601
-
Predicting disulfide connectivity patterns
-
Lu,C.H. et al. (2007) Predicting disulfide connectivity patterns. Proteins, 67, 262-270.
-
(2007)
Proteins
, vol.67
, pp. 262-270
-
-
Lu, C.H.1
-
29
-
-
0037162464
-
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds
-
Mallick,P. et al. (2002) Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl Acad. Sci. USA, 99, 9679-9684.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 9679-9684
-
-
Mallick, P.1
-
30
-
-
0032484157
-
Protein similarities beyond disulphide bridge topology
-
Mas,J.M. et al. (1998) Protein similarities beyond disulphide bridge topology. J. Mol. Biol., 284, 541-548.
-
(1998)
J. Mol. Biol
, vol.284
, pp. 541-548
-
-
Mas, J.M.1
-
31
-
-
0037083493
-
Predicting the disulfide bonding state of cysteines using protein descriptors
-
Mucchielli-Giorgi,M.H. et al. (2002) Predicting the disulfide bonding state of cysteines using protein descriptors. Proteins, 46, 243-249.
-
(2002)
Proteins
, vol.46
, pp. 243-249
-
-
Mucchielli-Giorgi, M.H.1
-
32
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin,A.G. et al. (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
-
33
-
-
0025118064
-
Prediction of the disulfide-bonding state of cysteine in proteins
-
Muskal,S.M. et al. (1990) Prediction of the disulfide-bonding state of cysteine in proteins. Protein Eng., 3, 667-672.
-
(1990)
Protein Eng
, vol.3
, pp. 667-672
-
-
Muskal, S.M.1
-
34
-
-
0028125904
-
How frequent are correlated changes in families of protein sequences?
-
Neher,E. (1994) How frequent are correlated changes in families of protein sequences? Proc. Natl Acad. Sci. USA, 91, 98-102.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 98-102
-
-
Neher, E.1
-
35
-
-
84984087977
-
Statistical mechanics of noncovalent bonds in polyamino acids. VIII. Covalent loops in proteins
-
Poland,D.C. and Scheraga,H.A. (1965) Statistical mechanics of noncovalent bonds in polyamino acids. VIII. Covalent loops in proteins. Biopolymers, 3, 379-399.
-
(1965)
Biopolymers
, vol.3
, pp. 379-399
-
-
Poland, D.C.1
Scheraga, H.A.2
-
36
-
-
33750414092
-
MMM: A sequence-to-structure alignment protocol
-
Rai,B.K. et al. (2006) MMM: A sequence-to-structure alignment protocol. Bioinformatics, 22, 2691-2692.
-
(2006)
Bioinformatics
, vol.22
, pp. 2691-2692
-
-
Rai, B.K.1
-
37
-
-
0028084754
-
Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
-
Shindyalov,I.N. et al. (1994) Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng., 7, 349-358.
-
(1994)
Protein Eng
, vol.7
, pp. 349-358
-
-
Shindyalov, I.N.1
-
38
-
-
0019881763
-
Disulphide bridges in globular proteins
-
Thornton,J.M. (1981) Disulphide bridges in globular proteins. J. Mol. Biol., 151, 261-287.
-
(1981)
J. Mol. Biol
, vol.151
, pp. 261-287
-
-
Thornton, J.M.1
-
39
-
-
28944438120
-
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines
-
Tsai,C.H. et al. (2005) Improving disulfide connectivity prediction with sequential distance between oxidized cysteines. Bioinformatics, 21, 4416-4419.
-
(2005)
Bioinformatics
, vol.21
, pp. 4416-4419
-
-
Tsai, C.H.1
-
40
-
-
1842455284
-
Disulfide connectivity prediction using recursive neural networks and evolutionary information
-
Vullo,A. and Frasconi,P. (2004) Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinformatics, 20, 653-659.
-
(2004)
Bioinformatics
, vol.20
, pp. 653-659
-
-
Vullo, A.1
Frasconi, P.2
-
41
-
-
0040786272
-
Disulfide bonds and protein folding
-
Wedemeyer,W.J. et al. (2000) Disulfide bonds and protein folding. Biochemistry, 39, 7032.
-
(2000)
Biochemistry
, vol.39
, pp. 7032
-
-
Wedemeyer, W.J.1
-
42
-
-
33846062023
-
Database resources of the National Center for Biotechnology Information
-
Wheeler,D.L. et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 35 D5-D12.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wheeler, D.L.1
-
43
-
-
17444411155
-
Cysteine separations profiles on protein sequences infer disulfide connectivity
-
Zhao,E. et al. (2005) Cysteine separations profiles on protein sequences infer disulfide connectivity. Bioinformatics, 21, 1415-1420.
-
(2005)
Bioinformatics
, vol.21
, pp. 1415-1420
-
-
Zhao, E.1
|