-
1
-
-
79952488320
-
Learning generative models for protein fold families
-
Balakrishnan,S. et al. (2011) Learning generative models for protein fold families. Proteins Struct Funct Bioinform., 79, 1061-1078.
-
(2011)
Proteins Struct Funct Bioinform.
, vol.79
, pp. 1061-1078
-
-
Balakrishnan, S.1
-
2
-
-
9144257886
-
The Pfam protein families database
-
Bateman,A. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32(Suppl. 1), D138-D141.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. D138-D141
-
-
Bateman, A.1
-
3
-
-
76749112068
-
Disentangling direct from indirect co-evolution of residues in protein alignments
-
Burger,L. and van Nimwegen, E. (2010) Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput. Biol., 6, e1000633.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Burger, L.1
Van Nimwegen, E.2
-
4
-
-
34247247779
-
Improved residue contact prediction using support vector machines and a large feature set
-
Cheng,J. and Baldi,P. (2007) Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics, 8, 113.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 113
-
-
Cheng, J.1
Baldi, P.2
-
5
-
-
84883427400
-
From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction
-
Cocco,S. et al. (2013) From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction. PLoS Comput. Biol., 9, e1003176.
-
(2013)
PLoS Comput. Biol.
, vol.9
-
-
Cocco, S.1
-
6
-
-
84893766307
-
The joint graphical lasso for inverse covariance estimation across multiple classes
-
Danaher,P. et al. (2014) The joint graphical lasso for inverse covariance estimation across multiple classes. J. Roy. Stat. Soc. B, 76, 373-397.
-
(2014)
J. Roy. Stat. Soc. B
, vol.76
, pp. 373-397
-
-
Danaher, P.1
-
7
-
-
84875225476
-
Emerging methods in protein co-evolution
-
de Juan,D. et al. (2013) Emerging methods in protein co-evolution. Nat. Rev. Genet., 14, 249-261.
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 249-261
-
-
De Juan, D.1
-
8
-
-
79957616537
-
Is there an optimal substitution matrix for contact prediction with correlated mutations?
-
Di Lena,P. et al. (2011) Is there an optimal substitution matrix for contact prediction with correlated mutations? IEEE/ACM Trans Comput. Biol. Bioinformatics, 8, 1017-1028.
-
(2011)
IEEE/ACM Trans Comput. Biol. Bioinformatics
, vol.8
, pp. 1017-1028
-
-
Di Lena, P.1
-
9
-
-
84867316765
-
Deep architectures for protein contact map prediction
-
Di Lena,P. et al. (2012) Deep architectures for protein contact map prediction. Bioinformatics, 28, 2449-2457.
-
(2012)
Bioinformatics
, vol.28
, pp. 2449-2457
-
-
Di Lena, P.1
-
10
-
-
33745783706
-
CONTRAlign: Discriminative training for protein sequence alignment
-
Springer
-
Do,C.B. et al. (2006) CONTRAlign: discriminative training for protein sequence alignment. In: Research in Computational Molecular Biology. Springer, pp. 160-174.
-
(2006)
Research in Computational Molecular Biology
, pp. 160-174
-
-
Do, C.B.1
-
11
-
-
38849115223
-
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
-
Dunn,S.D. et al. (2008) Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics, 24, 333-340.
-
(2008)
Bioinformatics
, vol.24
, pp. 333-340
-
-
Dunn, S.D.1
-
12
-
-
84870415234
-
Predicting protein residue-residue contacts using deep networks and boosting
-
Eickholt,J. and Cheng,J. (2012) Predicting protein residue-residue contacts using deep networks and boosting. Bioinformatics, 28, 3066-3072.
-
(2012)
Bioinformatics
, vol.28
, pp. 3066-3072
-
-
Eickholt, J.1
Cheng, J.2
-
13
-
-
84872521100
-
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
-
Ekeberg,M. et al. (2013) Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models. Phys. Rev. E, 87, 012707.
-
(2013)
Phys. Rev. E
, vol.87
-
-
Ekeberg, M.1
-
14
-
-
84891782659
-
Pfam: The protein families database
-
Finn,R.D. et al. (2014) Pfam: the protein families database. Nucleic Acids Res., 42, D222-D230.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
-
15
-
-
34548733641
-
The global trace graph, a novel paradigm for searching protein sequence databases
-
Heger,A. et al. (2007) The global trace graph, a novel paradigm for searching protein sequence databases. Bioinformatics, 23, 2361-2367.
-
(2007)
Bioinformatics
, vol.23
, pp. 2361-2367
-
-
Heger, A.1
-
16
-
-
0014604308
-
Multiplier and gradient methods
-
Hestenes,M.R. (1969) Multiplier and gradient methods. J. Optim. Theory Appl., 4, 303-320.
-
(1969)
J. Optim. Theory Appl.
, vol.4
, pp. 303-320
-
-
Hestenes, M.R.1
-
17
-
-
84862647180
-
Three-dimensional structures of membrane proteins from genomic sequencing
-
Hopf,T.A. et al. (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell, 149, 1607-1621.
-
(2012)
Cell
, vol.149
, pp. 1607-1621
-
-
Hopf, T.A.1
-
18
-
-
84856090271
-
PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
-
Jones,D.T. et al. (2012) PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics, 28, 184-190.
-
(2012)
Bioinformatics
, vol.28
, pp. 184-190
-
-
Jones, D.T.1
-
19
-
-
84929144039
-
MetaPSICOV: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
-
Jones, D.T. et al. (2015) MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics, 31, 999-1006.
-
(2015)
Bioinformatics
, vol.31
, pp. 999-1006
-
-
Jones, D.T.1
-
20
-
-
84884603324
-
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence-and structure-rich era
-
Kamisetty,H. et al. (2013) Assessing the utility of coevolution-based residue-residue contact predictions in a sequence-and structure-rich era. Proc. Natl Acad. Sci. USA, 110, 15674-15679.
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 15674-15679
-
-
Kamisetty, H.1
-
21
-
-
84892997887
-
One contact for every twelve residues allows robust and accurate topology-level protein structure modeling
-
Kim,D.E. et al. (2014) One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. Proteins, 82, 208-218.
-
(2014)
Proteins
, vol.82
, pp. 208-218
-
-
Kim, D.E.1
-
22
-
-
0141642142
-
ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
-
Klepeis,J. and Floudas,C. (2003) ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys. J., 85, 2119-2146.
-
(2003)
Biophys. J.
, vol.85
, pp. 2119-2146
-
-
Klepeis, J.1
Floudas, C.2
-
24
-
-
0008117663
-
Correlated mutations in models of protein sequences: Phylogenetic and structural effects
-
Lapedes,A.S. et al. (1999) Correlated mutations in models of protein sequences: phylogenetic and structural effects. Lecture Notes Monograph Series, 236-256.
-
(1999)
Lecture Notes Monograph Series
, pp. 236-256
-
-
Lapedes, A.S.1
-
26
-
-
82855163967
-
Protein 3D structure computed from evolutionary sequence variation
-
Marks,D.S. et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One, 6, e28766.
-
(2011)
PLoS One
, vol.6
-
-
Marks, D.S.1
-
27
-
-
84862192588
-
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
-
Nugent,T. and Jones,D.T. (2012) Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc. Natl Acad. Sci. USA, 109, E1540-E1547.
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. E1540-E1547
-
-
Nugent, T.1
Jones, D.T.2
-
28
-
-
79955715769
-
Multiple-template approach to protein threading
-
Peng,J. and Xu,J.A. (2011) multiple-template approach to protein threading. Proteins Struct. Funct. Bioinformatics, 79, 1930-1939.
-
(2011)
Proteins Struct. Funct. Bioinformatics
, vol.79
, pp. 1930-1939
-
-
Peng, J.1
Xu, J.A.2
-
29
-
-
84856489442
-
HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment
-
Remmert,M. et al. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173-175.
-
(2012)
Nat. Methods
, vol.9
, pp. 173-175
-
-
Remmert, M.1
-
31
-
-
84880209883
-
PconsC: Combination of direct information methods and alignments improves contact prediction
-
Skwark,M.J. et al. (2013) PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics, 29, 1815-1816.
-
(2013)
Bioinformatics
, vol.29
, pp. 1815-1816
-
-
Skwark, M.J.1
-
32
-
-
84912100015
-
Improved contact predictions using the recognition of protein like contact patterns
-
Skwark, M.J. et al. (2014) Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput. Biol., 10, e1003889.
-
(2014)
PLoS Comput. Biol.
, vol.10
-
-
Skwark, M.J.1
-
33
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
34
-
-
33746239564
-
Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences
-
Tan,Y.H. et al. (2006) Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins Struct. Funct. Bioinformatics, 64, 587-600.
-
(2006)
Proteins Struct. Funct. Bioinformatics
, vol.64
, pp. 587-600
-
-
Tan, Y.H.1
-
35
-
-
67849110005
-
NNcon: Improved protein contact map prediction using 2D-recursive neural networks
-
Tegge,A.N. et al. (2009) NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res., 37(Suppl. 2), W515-W518.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W515-W518
-
-
Tegge, A.N.1
-
37
-
-
68149166344
-
Graphical models of protein-protein interaction specificity from correlated mutations and interaction data
-
Thomas,J. et al. (2009) Graphical models of protein-protein interaction specificity from correlated mutations and interaction data. Proteins Struct. Funct. Bioinformatics, 76, 911-929.
-
(2009)
Proteins Struct. Funct. Bioinformatics
, vol.76
, pp. 911-929
-
-
Thomas, J.1
-
38
-
-
33645507429
-
M-Coffee: Combining multiple sequence alignment methods with T-Coffee
-
Wallace,I.M. et al. (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34, 1692-1699.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1692-1699
-
-
Wallace, I.M.1
-
39
-
-
84879976691
-
Predicting protein contact map using evolutionary and physical constraints by integer programming
-
Wang,Z. and Xu,J. (2013) Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics, 29, i266-i273.
-
(2013)
Bioinformatics
, vol.29
, pp. i266-i273
-
-
Wang, Z.1
Xu, J.2
-
40
-
-
58549114185
-
Identification of direct residue contacts in protein-protein interaction by message passing
-
Weigt,M. et al. (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc. Natl Acad. Sci. USA, 106, 67-72.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 67-72
-
-
Weigt, M.1
-
41
-
-
41349114023
-
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
-
Wu,S. and Zhang,Y. (2008) A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics, 24, 924-931.
-
(2008)
Bioinformatics
, vol.24
, pp. 924-931
-
-
Wu, S.1
Zhang, Y.2
-
42
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins Struct. Funct. Bioinformatics, 57, 702-710.
-
(2004)
Proteins Struct. Funct. Bioinformatics
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
43
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
Zhang,Y. and Skolnick,J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
44
-
-
84861977121
-
A position-specific distance-dependent statistical potential for protein structure and functional study
-
Zhao,F. and Xu,J. (2012) A position-specific distance-dependent statistical potential for protein structure and functional study. Structure, 20, 1118-1126.
-
(2012)
Structure
, vol.20
, pp. 1118-1126
-
-
Zhao, F.1
Xu, J.2
|