-
1
-
-
74049119478
-
DescFold: A web server for protein fold recognition
-
Yan, R.J.; Si, J.; Wang, C.; Zhang, Z. DescFold: A web server for protein fold recognition. BMC Bioinformatics, 2009, 10, 416.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 416
-
-
Yan, R.J.1
Si, J.2
Wang, C.3
Zhang, Z.4
-
2
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman, S.B.; Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 1970, 48(3), 443-453.
-
(1970)
J. Mol. Biol
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
3
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T.F.; Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol., 1981, 147(1), 195-197.
-
(1981)
J. Mol. Biol
, vol.147
, Issue.1
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol., 1990, 215(3), 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Pearson, W.R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 1990, 183, 63-98.
-
(1990)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
7
-
-
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., 1997, 25(17), 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, 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
-
8
-
-
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.; Altschul, S.F. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 1999, 15(12), 1000-1011.
-
(1999)
Bioinformatics
, vol.15
, Issue.12
, 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
-
9
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie, J.U.; Luthy, R.; Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science, 1991, 253, 164-169.
-
(1991)
Science
, vol.253
, pp. 164-169
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
10
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones, D.T.; Taylor, W.R.; Thornton, J.M. A new approach to protein fold recognition. Nature, 1992, 358(6381), 86-9.
-
(1992)
Nature
, vol.358
, Issue.6381
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
11
-
-
23144463912
-
FFAS03: A server for profile-profile sequence alignments
-
Jaroszewski, L.; Rychlewski, L.; Li, Z.; Li, W.; Godzik, A. FFAS03: a server for profile-profile sequence alignments. Nucleic. Acids Res., 2005, 33(suppl 2), W284-W288.
-
(2005)
Nucleic. Acids Res
, vol.33
, Issue.SUPPL. 2
-
-
Jaroszewski, L.1
Rychlewski, L.2
Li, Z.3
Li, W.4
Godzik, A.5
-
12
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelley, L.A.; MacCallum, R.M.; Sternberg, M.J. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol., 2000, 299(2), 499-520.
-
(2000)
J. Mol. Biol
, vol.299
, Issue.2
, pp. 499-520
-
-
Kelley, L.A.1
MacCallum, R.M.2
Sternberg, M.J.3
-
13
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi, J.; Blundell, T.L.; Mizuguchi, K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 2001, 310(1), 243-257.
-
(2001)
J. Mol. Biol
, vol.310
, Issue.1
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
14
-
-
0038634975
-
Improvement of the GenTHREADER method for genomic fold recognition
-
McGuffin, L.J.; Jones, D.T. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 2003, 19(7), 874-881.
-
(2003)
Bioinformatics
, vol.19
, Issue.7
, pp. 874-881
-
-
McGuffin, L.J.1
Jones, D.T.2
-
15
-
-
0042121000
-
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure
-
Ginalski, K.; Pas, J.; Wyrwicz, L.S.; von Grotthuss, M.; Bujnicki, J.M.; Rychlewski, L. ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic. Acids Res., 2004, 31(13), 3804-3807.
-
(2004)
Nucleic. Acids Res
, vol.31
, Issue.13
, pp. 3804-3807
-
-
Ginalski, K.1
Pas, J.2
Wyrwicz, L.S.3
Von Grotthuss, M.4
Bujnicki, J.M.5
Rychlewski, L.6
-
16
-
-
46449123146
-
MUSTER: Improving protein sequence profileprofile alignments by using multiple sources of structure information
-
Wu, S.; Zhang, Y. MUSTER: Improving protein sequence profileprofile alignments by using multiple sources of structure information. Proteins, 2008, 72(2), 547-556.
-
(2008)
Proteins
, vol.72
, Issue.2
, pp. 547-556
-
-
Wu, S.1
Zhang, Y.2
-
17
-
-
48449085801
-
SP5: Improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model
-
Zhang, W.; Liu, S.; Zhou, Y. SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. PLoS. ONE, 2008, 3(6), e2325.
-
(2008)
PLoS. ONE
, vol.3
, Issue.6
-
-
Zhang, W.1
Liu, S.2
Zhou, Y.3
-
18
-
-
84855703338
-
PSS-3D1D: An improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences
-
Ganesan, K.; Parthasarathy. S. PSS-3D1D: An improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences. J. Struct. Funct. Genomics, 2011, 12(4), 181-189.
-
(2011)
J. Struct. Funct. Genomics
, vol.12
, Issue.4
, pp. 181-189
-
-
Ganesan, K.1
Parthasarathy, S.2
-
19
-
-
84995072940
-
Protein fold prediction from secondary structure assignment
-
IEEE press.
-
Russell, R.B.; Copley, R.R.; Barton, G.J. Protein fold prediction from secondary structure assignment, Proc. 29th Ann. Hawaii. Int. Conf. Sys. Sci., IEEE press. 1995, V, 302-311.
-
(1995)
Proc. 29th Ann. Hawaii. Int. Conf. Sys. Sci.
, vol.5
, pp. 302-311
-
-
Russell, R.B.1
Copley, R.R.2
Barton, G.J.3
-
20
-
-
41149162869
-
Local protein structures
-
Offmann, B.; Tyagi, M.; de Brevern, A.G. Local protein structures. Curr. Bioinf., 2007, 3, 165-202.
-
(2007)
Curr. Bioinf
, vol.3
, pp. 165-202
-
-
Offmann, B.1
Tyagi, M.2
De Brevern, A.G.3
-
21
-
-
0034669774
-
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
-
de Brevern, A.G.; Etchebest, C.; Hazout, S. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins, 2000, 41, 271-287.
-
(2000)
Proteins
, vol.41
, pp. 271-287
-
-
De Brevern, A.G.1
Etchebest, C.2
Hazout, S.3
-
22
-
-
23144437382
-
New assessment of a structural alphabet
-
de Brevern, A.G. New assessment of a structural alphabet. In. Silico. Biol., 2005, 5, 283-289.
-
(2005)
In. Silico. Biol
, vol.5
, pp. 283-289
-
-
De Brevern, A.G.1
-
23
-
-
0036893073
-
Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship
-
de Brevern, A.G.; Valadie, H.; Hazout, S.; Etchebest, C. Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. Protein Sci., 2002, 11, 2871-2886.
-
(2002)
Protein Sci
, vol.11
, pp. 2871-2886
-
-
De Brevern, A.G.1
Valadie, H.2
Hazout, S.3
Etchebest, C.4
-
24
-
-
33947526348
-
"Pinning strategy": A novel approach for predicting the backbone structure in terms of protein blocks from sequence
-
de Brevern, A.G.; Etchebest, C.; Benros, C.; Hazout, S. "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. J. Biosci., 2007, 32, 51-70.
-
(2007)
J. Biosci
, vol.32
, pp. 51-70
-
-
De Brevern, A.G.1
Etchebest, C.2
Benros, C.3
Hazout, S.4
-
25
-
-
79551489873
-
A short survey on Protein Blocks
-
Joseph, A.P.; Agarwal, G.; Mahajan, S.; Gelly, J.C.; Swapna, L.S.; Offmann, B.; Cadet, F.; Bornot, A.; Tyagi, M.; Valadié, H.; Schneider, B.; Etchebest, C.; Srinivasan, N.; de Brevern, A.G. A short survey on Protein Blocks. Biophys. Rev., 2010, 2(3), 137-145.
-
(2010)
Biophys. Rev
, vol.2
, Issue.3
, pp. 137-145
-
-
Joseph, A.P.1
Agarwal, G.2
Mahajan, S.3
Gelly, J.C.4
Swapna, L.S.5
Offmann, B.6
Cadet, F.7
Bornot, A.8
Tyagi, M.9
Valadié, H.10
Schneider, B.11
Etchebest, C.12
Srinivasan, N.13
De Brevern, A.G.14
-
26
-
-
33644840330
-
Assessing a novel approach for predicting local 3D protein structures from sequence
-
Benros, C.; de Brevern, A.G.; Etchebest, C.; Hazout, S. Assessing a novel approach for predicting local 3D protein structures from sequence. Proteins, 2006, 62, 865-880.
-
(2006)
Proteins
, vol.62
, pp. 865-880
-
-
Benros, C.1
De Brevern, A.G.2
Etchebest, C.3
Hazout, S.4
-
27
-
-
57749200715
-
Analyzing the sequence structure relationship of a library of local structural prototypes
-
Benros, C.; de Brevern, A.G.; Hazout, S. Analyzing the sequence structure relationship of a library of local structural prototypes. J. Theor. Biol., 2009, 256, 215-226.
-
(2009)
J. Theor. Biol
, vol.256
, pp. 215-226
-
-
Benros, C.1
De Brevern, A.G.2
Hazout, S.3
-
28
-
-
68049131595
-
A new prediction strategy for long local protein structures using an original description
-
Bornot, A.; Etchebest, C.; de Brevern, A.G. A new prediction strategy for long local protein structures using an original description. Proteins, 2009, 76, 570-587.
-
(2009)
Proteins
, vol.76
, pp. 570-587
-
-
Bornot, A.1
Etchebest, C.2
De Brevern, A.G.3
-
29
-
-
0001840836
-
Hybrid protein model (HPM): A method to compact protein 3D-structures information and physicochemical properties
-
de Brevern, A.G.; Hazout, S. Hybrid Protein Model (HPM): a method to compact protein 3D-structures information and physicochemical properties. IEEE-Computer. Soc., 2000, S1, 49-54.
-
(2000)
IEEE-Computer. Soc
, vol.S1
, pp. 49-54
-
-
De Brevern, A.G.1
Hazout, S.2
-
30
-
-
0037433050
-
'Hybrid protein model' for optimally defining 3D protein structure fragments
-
de Brevern, A.G.; Hazout, S. 'Hybrid protein model' for optimally defining 3D protein structure fragments. Bioinformatics, 2003, 19, 345-353.
-
(2003)
Bioinformatics
, vol.19
, pp. 345-353
-
-
De Brevern, A.G.1
Hazout, S.2
-
31
-
-
2942541294
-
Use of a structural alphabet for analysis of short loops connecting repetitive structures
-
Fourrier, L.; Benros, C.; de Brevern, A.G. Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinformatics, 2004, 5, 58.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 58
-
-
Fourrier, L.1
Benros, C.2
De Brevern, A.G.3
-
32
-
-
77950542887
-
Analysis of loop boundaries using different local structure assignment methods
-
Tyagi, M.; Bornot, A.; Offmann, B.; de Brevern, A.G. Analysis of loop boundaries using different local structure assignment methods. Protein Sci., 2009, 18, 1869-1881.
-
(2009)
Protein Sci
, vol.18
, pp. 1869-1881
-
-
Tyagi, M.1
Bornot, A.2
Offmann, B.3
De Brevern, A.G.4
-
33
-
-
68949178663
-
Protein short loop prediction in terms of a structural alphabet
-
Tyagi, M.; Bornot, A.; Offmann, B.; de Brevern, A.G. Protein short loop prediction in terms of a structural alphabet. Comput. Biol. Chem., 2009, 33, 329-333.
-
(2009)
Comput. Biol. Chem
, vol.33
, pp. 329-333
-
-
Tyagi, M.1
Bornot, A.2
Offmann, B.3
De Brevern, A.G.4
-
34
-
-
41149083129
-
Protein contacts, interresidue interactions and side-chain modelling
-
Faure, G.; Bornot, A.; de Brevern, A.G. Protein contacts, interresidue interactions and side-chain modelling. Biochimie, 2008, 90, 626-639.
-
(2008)
Biochimie
, vol.90
, pp. 626-639
-
-
Faure, G.1
Bornot, A.2
De Brevern, A.G.3
-
35
-
-
34548406068
-
Methods for optimizing the structure alphabet sequences of proteins
-
Dong, Q.W.; Wang, X.L.; Lin, L. Methods for optimizing the structure alphabet sequences of proteins. Comput. Biol., 2007, 37, 1610-1616.
-
(2007)
Comput. Biol
, vol.37
, pp. 1610-1616
-
-
Dong, Q.W.1
Wang, X.L.2
Lin, L.3
-
36
-
-
67650652199
-
New opportunities to fight against infectious diseases and to identify pertinent drug targets with novel methodologies
-
de Brevern, A.G. New opportunities to fight against infectious diseases and to identify pertinent drug targets with novel methodologies. Infect. Disord. Drug Targets, 2009, 9, 246-247.
-
(2009)
Infect. Disord. Drug Targets
, vol.9
, pp. 246-247
-
-
De Brevern, A.G.1
-
37
-
-
67650677034
-
In silico studies on DARC
-
de Brevern, A.G.; Autin, L.; Colin, Y.; Bertrand, O.; Etchebest, C. In silico studies on DARC. Infect. Disord. Drug Targets, 2009, 9, 289-303.
-
(2009)
Infect. Disord. Drug Targets
, vol.9
, pp. 289-303
-
-
De Brevern, A.G.1
Autin, L.2
Colin, Y.3
Bertrand, O.4
Etchebest, C.5
-
38
-
-
23144464778
-
A structural model of a seventransmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC)
-
de Brevern, A.G.; Wong, H.; Tournamille, C.; Colin, Y.; Le Van Kim, C.; Etchebest, C. A structural model of a seventransmembrane helix receptor: the Duffy antigen/receptor for chemokine (DARC). Biochim. Biophys. Acta, 2005, 1724(3), 288-306.
-
(2005)
Biochim. Biophys. Acta
, vol.1724
, Issue.3
, pp. 288-306
-
-
De Brevern, A.G.1
Wong, H.2
Tournamille, C.3
Colin, Y.4
Le Van Kim, C.5
Etchebest, C.6
-
39
-
-
34147202792
-
Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites
-
Dudev, M.; Lim, C. Discovering structural motifs using a structural alphabet: application to magnesium-binding sites. BMC Bioinformatics, 2007, 8, 106.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 106
-
-
Dudev, M.1
Lim, C.2
-
40
-
-
35748976251
-
A reduced amino acid alphabet for understanding and designing protein adaptation to mutation
-
Etchebest, C.; Benros, C.; Bornot, A.; Camproux, A.C.; de Brevern, A.G. A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. Eur. Biophys. J., 2007, 36, 1059-1069.
-
(2007)
Eur. Biophys. J
, vol.36
, pp. 1059-1069
-
-
Etchebest, C.1
Benros, C.2
Bornot, A.3
Camproux, A.C.4
De Brevern, A.G.5
-
41
-
-
33748280492
-
A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
-
Tyagi, M.; Gowri, V.S.; Srinivasan, N.; de Brevern, A.G.; Offmann, B. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications. Proteins, 2006, 65, 32-39.
-
(2006)
Proteins
, vol.65
, pp. 32-39
-
-
Tyagi, M.1
Gowri, V.S.2
Srinivasan, N.3
De Brevern, A.G.4
Offmann, B.5
-
42
-
-
33747831751
-
Protein Block Expert (PBE): A webbased protein structure analysis server using a structural alphabet
-
Tyagi, M.; Sharma, P.; Swamy, C.S.; Cadet, F.; Srinivasan, N.; de Brevern, A.G.; Offmann, B. Protein Block Expert (PBE): a webbased protein structure analysis server using a structural alphabet. Nucleic Acids Res., 2006, 34, W119-W123.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Tyagi, M.1
Sharma, P.2
Swamy, C.S.3
Cadet, F.4
Srinivasan, N.5
De Brevern, A.G.6
Offmann, B.7
-
43
-
-
41149118582
-
Protein structure mining using a structural alphabet
-
Tyagi, M.; de Brevern, A.G.; Srinivasan, N.; Offmann, B. Protein structure mining using a structural alphabet. Proteins, 2008, 71, 920-937.
-
(2008)
Proteins
, vol.71
, pp. 920-937
-
-
Tyagi, M.1
De Brevern, A.G.2
Srinivasan, N.3
Offmann, B.4
-
44
-
-
0038278386
-
Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry
-
Karchin, R.; Cline, M.; Mandel-Gutfreund, Y.; Karplus, K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins, 2003, 51, 504-514.
-
(2003)
Proteins
, vol.51
, pp. 504-514
-
-
Karchin, R.1
Cline, M.2
Mandel-Gutfreund, Y.3
Karplus, K.4
-
45
-
-
84877941568
-
-
http://bioinformatics.univ-reunion.fr/PBE/pb-prediction/
-
-
-
-
46
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.G.; Brenner, S.E.; Hubbard, T.; Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 1995, 247(4), 536-40.
-
(1995)
J. Mol. Biol
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
47
-
-
0033954256
-
The protein data bank
-
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res., 2000, 28, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
48
-
-
0031453963
-
OLDERADO: On-line database of ensemble representatives and domains
-
Kelley, L.A.; Sutcliffe, M.J. OLDERADO: on-line database of ensemble representatives and domains. Protein Sci., 1997, 6(12), 2628-2630.
-
(1997)
Protein Sci
, vol.6
, Issue.12
, pp. 2628-2630
-
-
Kelley, L.A.1
Sutcliffe, M.J.2
-
49
-
-
0032512799
-
Empirical statistical estimates for sequence similarity searches
-
Pearson, W.R. Empirical statistical estimates for sequence similarity searches. J. Mol. Biol., 1998, 276, 71-84.
-
(1998)
J. Mol. Biol
, vol.276
, pp. 71-84
-
-
Pearson, W.R.1
-
50
-
-
33748809505
-
Statistical significance in biological sequence analysis
-
Mitrophanov, A.Y.; Borodovsky, M. Statistical significance in biological sequence analysis. Briefings. Bioinf., 2006, 7, 2-24.
-
(2006)
Briefings. Bioinf
, vol.7
, pp. 2-24
-
-
Mitrophanov, A.Y.1
Borodovsky, M.2
-
51
-
-
0001969211
-
Use of receiver operating characteristic (roc) analysis to evaluate sequence matching
-
Gribskov, M.; Robinson, N.L. Use of receiver operating characteristic (roc) analysis to evaluate sequence matching. Comput. Chem., 1996, 20, 25-33.
-
(1996)
Comput. Chem
, vol.20
, pp. 25-33
-
-
Gribskov, M.1
Robinson, N.L.2
|