-
1
-
-
84934440243
-
MAFFT: iterative refinement and additional methods
-
Katoh K., Standley D.M. MAFFT: iterative refinement and additional methods. Methods Mol Biol 2014, 1079:131-146.
-
(2014)
Methods Mol Biol
, vol.1079
, pp. 131-146
-
-
Katoh, K.1
Standley, D.M.2
-
2
-
-
84934435406
-
Clustal omega, accurate alignment of very large numbers of sequences
-
Sievers F., Higgins D.G. Clustal omega, accurate alignment of very large numbers of sequences. Methods Mol Biol 2014, 1079:105-116.
-
(2014)
Methods Mol Biol
, vol.1079
, pp. 105-116
-
-
Sievers, F.1
Higgins, D.G.2
-
3
-
-
84891782659
-
Pfam: the protein families database
-
Finn R.D., Bateman A., Clements J., Coggill P., Eberhardt R.Y., Eddy S.R., Heger A., Hetherington K., Holm L., Mistry J., Sonnhammer E.L., et al. Pfam: the protein families database. Nucleic Acids Res 2014, 42:D222-D230.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D222-D230
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
Heger, A.7
Hetherington, K.8
Holm, L.9
Mistry, J.10
Sonnhammer, E.L.11
-
4
-
-
84941042486
-
CDD: NCBI's conserved domain database
-
Marchler-Bauer A., Derbyshire M.K., Gonzales N.R., Lu S., Chitsaz F., Geer L.Y., Geer R.C., He J., Gwadz M., Hurwitz D.I., Lanczycki C.J., et al. CDD: NCBI's conserved domain database. Nucleic Acids Res 2015, 43:D222-D226.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D222-D226
-
-
Marchler-Bauer, A.1
Derbyshire, M.K.2
Gonzales, N.R.3
Lu, S.4
Chitsaz, F.5
Geer, L.Y.6
Geer, R.C.7
He, J.8
Gwadz, M.9
Hurwitz, D.I.10
Lanczycki, C.J.11
-
5
-
-
77952988108
-
A new generation of homology search tools based on probabilistic inference
-
Eddy S.R. A new generation of homology search tools based on probabilistic inference. Genome Inf 2009, 23:205-211.
-
(2009)
Genome Inf
, vol.23
, pp. 205-211
-
-
Eddy, S.R.1
-
6
-
-
84941349095
-
HMMER web server: 2015 update
-
Finn R.D., Clements J., Arndt W., Miller B.L., Wheeler T.J., Schreiber F., Bateman A., Eddy S.R. HMMER web server: 2015 update. Nucleic Acids Res 2015, 43:W30-W38.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. W30-W38
-
-
Finn, R.D.1
Clements, J.2
Arndt, W.3
Miller, B.L.4
Wheeler, T.J.5
Schreiber, F.6
Bateman, A.7
Eddy, S.R.8
-
7
-
-
84856489442
-
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
-
Remmert M., Biegert A., Hauser A., Soding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 2012, 9:173-175.
-
(2012)
Nat Methods
, vol.9
, pp. 173-175
-
-
Remmert, M.1
Biegert, A.2
Hauser, A.3
Soding, J.4
-
8
-
-
84901271941
-
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction
-
Yan R., Xu D., Yang J., Walker S., Zhang Y. A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep 2013, 3:2619.
-
(2013)
Sci Rep
, vol.3
, pp. 2619
-
-
Yan, R.1
Xu, D.2
Yang, J.3
Walker, S.4
Zhang, Y.5
-
9
-
-
67650751542
-
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
-
Neuwald A.F. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinformatics 2009, 25:1869-1875.
-
(2009)
Bioinformatics
, vol.25
, pp. 1869-1875
-
-
Neuwald, A.F.1
-
10
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
Lockless S.W., Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999, 286:295-299.
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
11
-
-
68749107059
-
Protein sectors: evolutionary units of three-dimensional structure
-
Halabi N., Rivoire O., Leibler S., Ranganathan R. Protein sectors: evolutionary units of three-dimensional structure. Cell 2009, 138:774-786.
-
(2009)
Cell
, vol.138
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
12
-
-
84874029754
-
Evolution-based design of proteins
-
Reynolds K.A., Russ W.P., Socolich M., Ranganathan R. Evolution-based design of proteins. Methods Enzymol 2013, 523:213-235.
-
(2013)
Methods Enzymol
, vol.523
, pp. 213-235
-
-
Reynolds, K.A.1
Russ, W.P.2
Socolich, M.3
Ranganathan, R.4
-
13
-
-
84455167671
-
Hot spots for allosteric regulation on protein surfaces
-
Reynolds K.A., McLaughlin R.N., Ranganathan R. Hot spots for allosteric regulation on protein surfaces. Cell 2011, 147:1564-1575.
-
(2011)
Cell
, vol.147
, pp. 1564-1575
-
-
Reynolds, K.A.1
McLaughlin, R.N.2
Ranganathan, R.3
-
14
-
-
84891465457
-
Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis
-
Tanwar A.S., Goyal V.D., Choudhary D., Panjikar S., Anand R. Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis. PLOS ONE 2013, 8:e77781.
-
(2013)
PLOS ONE
, vol.8
, pp. e77781
-
-
Tanwar, A.S.1
Goyal, V.D.2
Choudhary, D.3
Panjikar, S.4
Anand, R.5
-
15
-
-
84944474861
-
Protein sectors: statistical coupling analysis versus conservation
-
Tesileanu T., Colwell L.J., Leibler S. Protein sectors: statistical coupling analysis versus conservation. PLoS Comput Biol 2015, 11:e1004091.
-
(2015)
PLoS Comput Biol
, vol.11
, pp. e1004091
-
-
Tesileanu, T.1
Colwell, L.J.2
Leibler, S.3
-
16
-
-
76649113438
-
Protein interactions and ligand binding: from protein subfamilies to functional specificity
-
Rausell A., Juan D., Pazos F., Valencia A. Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A 2010, 107:1995-2000.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 1995-2000
-
-
Rausell, A.1
Juan, D.2
Pazos, F.3
Valencia, A.4
-
17
-
-
84875225476
-
Emerging methods in protein co-evolution
-
de Juan D., Pazos F., Valencia A. Emerging methods in protein co-evolution. Nat Rev Genet 2013, 14:249-261.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 249-261
-
-
de Juan, D.1
Pazos, F.2
Valencia, A.3
-
18
-
-
84883427400
-
From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction
-
Cocco S., Monasson R., Weigt M. From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol 2013, 9:e1003176.
-
(2013)
PLoS Comput Biol
, vol.9
, pp. e1003176
-
-
Cocco, S.1
Monasson, R.2
Weigt, M.3
-
19
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
Morcos F., Pagnani A., Lunt B., Bertolino A., Marks D.S., Sander C., Zecchina R., Onuchic J.N., Hwa T., Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A 2011, 108:E1293-E1301.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. E1293-E1301
-
-
Morcos, F.1
Pagnani, A.2
Lunt, B.3
Bertolino, A.4
Marks, D.S.5
Sander, C.6
Zecchina, R.7
Onuchic, J.N.8
Hwa, T.9
Weigt, M.10
-
20
-
-
84856090271
-
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
-
Jones D.T., Buchan D.W., Cozzetto D., Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 2012, 28:184-190.
-
(2012)
Bioinformatics
, vol.28
, pp. 184-190
-
-
Jones, D.T.1
Buchan, D.W.2
Cozzetto, D.3
Pontil, M.4
-
21
-
-
84869447010
-
Protein structure prediction from sequence variation
-
Marks D.S., Hopf T.A., Sander C. Protein structure prediction from sequence variation. Nat Biotechnol 2012, 30:1072-1080.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 1072-1080
-
-
Marks, D.S.1
Hopf, T.A.2
Sander, C.3
-
22
-
-
84907863038
-
Direct coupling analysis for protein contact prediction
-
Morcos F., Hwa T., Onuchic J.N., Weigt M. Direct coupling analysis for protein contact prediction. Methods Mol Biol 2014, 1137:55-70.
-
(2014)
Methods Mol Biol
, vol.1137
, pp. 55-70
-
-
Morcos, F.1
Hwa, T.2
Onuchic, J.N.3
Weigt, M.4
-
23
-
-
84938651255
-
Inferring pairwise interactions from biological data using maximum-entropy probability models
-
Stein R.R., Marks D.S., Sander C. Inferring pairwise interactions from biological data using maximum-entropy probability models. PLoS Comput Biol 2015, 11:e1004182.
-
(2015)
PLoS Comput Biol
, vol.11
, pp. e1004182
-
-
Stein, R.R.1
Marks, D.S.2
Sander, C.3
-
24
-
-
79952488320
-
Learning generative models for protein fold families
-
Balakrishnan S., Kamisetty H., Carbonell J.G., Lee S.I., Langmead C.J. Learning generative models for protein fold families. Proteins 2011, 79:1061-1078.
-
(2011)
Proteins
, vol.79
, pp. 1061-1078
-
-
Balakrishnan, S.1
Kamisetty, H.2
Carbonell, J.G.3
Lee, S.I.4
Langmead, C.J.5
-
25
-
-
84899707813
-
Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners
-
Baldassi C., Zamparo M., Feinauer C., Procaccini A., Zecchina R., Weigt M., Pagnani A. Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners. PLOS ONE 2014, 9:e92721.
-
(2014)
PLOS ONE
, vol.9
, pp. e92721
-
-
Baldassi, C.1
Zamparo, M.2
Feinauer, C.3
Procaccini, A.4
Zecchina, R.5
Weigt, M.6
Pagnani, A.7
-
26
-
-
84908313189
-
Improving contact prediction along three dimensions
-
Feinauer C., Skwark M.J., Pagnani A., Aurell E. Improving contact prediction along three dimensions. PLoS Comput Biol 2014, 10:e1003847.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003847
-
-
Feinauer, C.1
Skwark, M.J.2
Pagnani, A.3
Aurell, E.4
-
27
-
-
84907031199
-
PconsFold: improved contact predictions improve protein models
-
Michel M., Hayat S., Skwark M.J., Sander C., Marks D.S., Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics 2014, 30:i482-i488.
-
(2014)
Bioinformatics
, vol.30
, pp. i482-i488
-
-
Michel, M.1
Hayat, S.2
Skwark, M.J.3
Sander, C.4
Marks, D.S.5
Elofsson, A.6
-
28
-
-
84911444768
-
CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations
-
Seemayer S., Gruber M., Soding J. CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics 2014, 30:3128-3130.
-
(2014)
Bioinformatics
, vol.30
, pp. 3128-3130
-
-
Seemayer, S.1
Gruber, M.2
Soding, J.3
-
29
-
-
84929144039
-
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
-
Jones D.T., Singh T., Kosciolek T., Tetchner S. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics 2015, 31:999-1006.
-
(2015)
Bioinformatics
, vol.31
, pp. 999-1006
-
-
Jones, D.T.1
Singh, T.2
Kosciolek, T.3
Tetchner, S.4
-
30
-
-
84899072164
-
FreeContact: fast and free software for protein contact prediction from residue co-evolution
-
Kajan L., Hopf T.A., Kalas M., Marks D.S., Rost B. FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinf 2014, 15:85.
-
(2014)
BMC Bioinf
, vol.15
, pp. 85
-
-
Kajan, L.1
Hopf, T.A.2
Kalas, M.3
Marks, D.S.4
Rost, B.5
-
31
-
-
84862647180
-
Three-dimensional structures of membrane proteins from genomic sequencing
-
Hopf T.A., Colwell L.J., Sheridan R., Rost B., Sander C., Marks D.S. Three-dimensional structures of membrane proteins from genomic sequencing. Cell 2012, 149:1607-1621.
-
(2012)
Cell
, vol.149
, pp. 1607-1621
-
-
Hopf, T.A.1
Colwell, L.J.2
Sheridan, R.3
Rost, B.4
Sander, C.5
Marks, D.S.6
-
32
-
-
84923079683
-
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors
-
Hopf T.A., Morinaga S., Ihara S., Touhara K., Marks D.S., Benton R. Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors. Nat Commun 2015, 6:6077.
-
(2015)
Nat Commun
, vol.6
, pp. 6077
-
-
Hopf, T.A.1
Morinaga, S.2
Ihara, S.3
Touhara, K.4
Marks, D.S.5
Benton, R.6
-
33
-
-
84928651779
-
All-atom 3D structure prediction of transmembrane beta-barrel proteins from sequences
-
Hayat S., Sander C., Marks D.S., Elofsson A. All-atom 3D structure prediction of transmembrane beta-barrel proteins from sequences. Proc Natl Acad Sci U S A 2015, 112:5413-5418.
-
(2015)
Proc Natl Acad Sci U S A
, vol.112
, pp. 5413-5418
-
-
Hayat, S.1
Sander, C.2
Marks, D.S.3
Elofsson, A.4
-
34
-
-
84884962856
-
Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis
-
Dwyer R.S., Ricci D.P., Colwell L.J., Silhavy T.J., Wingreen N.S. Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics 2013, 195:443-455.
-
(2013)
Genetics
, vol.195
, pp. 443-455
-
-
Dwyer, R.S.1
Ricci, D.P.2
Colwell, L.J.3
Silhavy, T.J.4
Wingreen, N.S.5
-
35
-
-
84934269306
-
Capturing coevolutionary signals in repeat proteins
-
Espada R., Parra R.G., Mora T., Walczak A.M., Ferreiro D.U. Capturing coevolutionary signals in repeat proteins. BMC Bioinf 2015, 16:207.
-
(2015)
BMC Bioinf
, vol.16
, pp. 207
-
-
Espada, R.1
Parra, R.G.2
Mora, T.3
Walczak, A.M.4
Ferreiro, D.U.5
-
36
-
-
84994885238
-
Sequence co-evolution gives 3D contacts and structures of protein complexes
-
Hopf T.A., Scharfe C.P., Rodrigues J.P., Green A.G., Kohlbacher O., Sander C., Bonvin A.M., Marks D.S. Sequence co-evolution gives 3D contacts and structures of protein complexes. Elife 2014, 3.
-
(2014)
Elife
, vol.3
-
-
Hopf, T.A.1
Scharfe, C.P.2
Rodrigues, J.P.3
Green, A.G.4
Kohlbacher, O.5
Sander, C.6
Bonvin, A.M.7
Marks, D.S.8
-
37
-
-
84941010317
-
Dimeric interactions and complex formation using direct coevolutionary couplings
-
dos Santos R.N., Morcos F., Jana B., Andricopulo A.D., Onuchic J.N. Dimeric interactions and complex formation using direct coevolutionary couplings. Sci Rep 2015, 5:13652.
-
(2015)
Sci Rep
, vol.5
, pp. 13652
-
-
dos Santos, R.N.1
Morcos, F.2
Jana, B.3
Andricopulo, A.D.4
Onuchic, J.N.5
-
38
-
-
84946122283
-
Structure and sequence analyses of clustered protocadherins reveal antiparallel interactions that mediate homophilic specificity
-
Nicoludis J.M., Lau S.Y., Scharfe C.P., Marks D.S., Weihofen W.A., Gaudet R. Structure and sequence analyses of clustered protocadherins reveal antiparallel interactions that mediate homophilic specificity. Structure 2015, 23:2087-2098.
-
(2015)
Structure
, vol.23
, pp. 2087-2098
-
-
Nicoludis, J.M.1
Lau, S.Y.2
Scharfe, C.P.3
Marks, D.S.4
Weihofen, W.A.5
Gaudet, R.6
-
39
-
-
84893476565
-
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
-
Cheng R.R., Morcos F., Levine H., Onuchic J.N. Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc Natl Acad Sci U S A 2014, 111:E563-E571.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. E563-E571
-
-
Cheng, R.R.1
Morcos, F.2
Levine, H.3
Onuchic, J.N.4
-
40
-
-
84960426522
-
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species
-
Avila-Herrera A., Pollard K.S. Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinf 2015, 16:268.
-
(2015)
BMC Bioinf
, vol.16
, pp. 268
-
-
Avila-Herrera, A.1
Pollard, K.S.2
-
41
-
-
84931078182
-
Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution
-
Mao W., Kaya C., Dutta A., Horovitz A., Bahar I. Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinformatics 2015, 31:1929-1937.
-
(2015)
Bioinformatics
, vol.31
, pp. 1929-1937
-
-
Mao, W.1
Kaya, C.2
Dutta, A.3
Horovitz, A.4
Bahar, I.5
-
42
-
-
84902081454
-
Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments
-
Clark G.W., Ackerman S.H., Tillier E.R., Gatti D.L. Multidimensional mutual information methods for the analysis of covariation in multiple sequence alignments. BMC Bioinf 2014, 15:157.
-
(2014)
BMC Bioinf
, vol.15
, pp. 157
-
-
Clark, G.W.1
Ackerman, S.H.2
Tillier, E.R.3
Gatti, D.L.4
-
43
-
-
84949027135
-
Covariation is a poor measure of molecular coevolution
-
Talavera D., Lovell S.C., Whelan S. Covariation is a poor measure of molecular coevolution. Mol Biol Evol 2015, 32:2456-2468.
-
(2015)
Mol Biol Evol
, vol.32
, pp. 2456-2468
-
-
Talavera, D.1
Lovell, S.C.2
Whelan, S.3
-
44
-
-
84946595514
-
From residue coevolution to protein conformational ensembles and functional dynamics
-
Sutto L., Marsili S., Valencia A., Gervasio F.L. From residue coevolution to protein conformational ensembles and functional dynamics. Proc Natl Acad Sci U S A 2015, 112:13567-13572.
-
(2015)
Proc Natl Acad Sci U S A
, vol.112
, pp. 13567-13572
-
-
Sutto, L.1
Marsili, S.2
Valencia, A.3
Gervasio, F.L.4
-
45
-
-
84941313519
-
Conformational dynamics of response regulator RegX3 from Mycobacterium tuberculosis
-
Ahmad A., Cai Y., Chen X., Shuai J., Han A. Conformational dynamics of response regulator RegX3 from Mycobacterium tuberculosis. PLOS ONE 2015, 10:e0133389.
-
(2015)
PLOS ONE
, vol.10
, pp. e0133389
-
-
Ahmad, A.1
Cai, Y.2
Chen, X.3
Shuai, J.4
Han, A.5
-
46
-
-
84951908781
-
Large-scale conformational transitions and dimerization are encoded in the amino-acid sequences of Hsp70 chaperones
-
Malinverni D., Marsili S., Barducci A., De Los Rios P. Large-scale conformational transitions and dimerization are encoded in the amino-acid sequences of Hsp70 chaperones. PLoS Comput Biol 2015, 11:e1004262.
-
(2015)
PLoS Comput Biol
, vol.11
, pp. e1004262
-
-
Malinverni, D.1
Marsili, S.2
Barducci, A.3
De Los Rios, P.4
-
47
-
-
84884603324
-
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
-
Kamisetty H., Ovchinnikov S., Baker D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci U S A 2013, 110:15674-15679.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 15674-15679
-
-
Kamisetty, H.1
Ovchinnikov, S.2
Baker, D.3
-
48
-
-
84885431817
-
High-resolution comparative modeling with RosettaCM
-
Song Y., DiMaio F., Wang R.Y., Kim D., Miles C., Brunette T., Thompson J., Baker D. High-resolution comparative modeling with RosettaCM. Structure 2013, 21:1735-1742.
-
(2013)
Structure
, vol.21
, pp. 1735-1742
-
-
Song, Y.1
DiMaio, F.2
Wang, R.Y.3
Kim, D.4
Miles, C.5
Brunette, T.6
Thompson, J.7
Baker, D.8
-
49
-
-
84937459728
-
Computation and functional studies provide a model for the structure of the zinc transporter hZIP4
-
Antala S., Ovchinnikov S., Kamisetty H., Baker D., Dempski R.E. Computation and functional studies provide a model for the structure of the zinc transporter hZIP4. J Biol Chem 2015, 290:17796-17805.
-
(2015)
J Biol Chem
, vol.290
, pp. 17796-17805
-
-
Antala, S.1
Ovchinnikov, S.2
Kamisetty, H.3
Baker, D.4
Dempski, R.E.5
-
50
-
-
84945928515
-
Large-scale determination of previously unsolved protein structures using evolutionary information
-
Ovchinnikov S., Kinch L., Park H., Liao Y., Pei J., Kim D.E., Kamisetty H., Grishin N.V., Baker D. Large-scale determination of previously unsolved protein structures using evolutionary information. Elife 2015, 4.
-
(2015)
Elife
, vol.4
-
-
Ovchinnikov, S.1
Kinch, L.2
Park, H.3
Liao, Y.4
Pei, J.5
Kim, D.E.6
Kamisetty, H.7
Grishin, N.V.8
Baker, D.9
-
52
-
-
84898619057
-
De novo structure prediction of globular proteins aided by sequence variation-derived contacts
-
Kosciolek T., Jones D.T. De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PLOS ONE 2014, 9:e92197.
-
(2014)
PLOS ONE
, vol.9
, pp. e92197
-
-
Kosciolek, T.1
Jones, D.T.2
-
53
-
-
84908542331
-
Combining physicochemical and evolutionary information for protein contact prediction
-
Schneider M., Brock O. Combining physicochemical and evolutionary information for protein contact prediction. PLOS ONE 2014, 9:e108438.
-
(2014)
PLOS ONE
, vol.9
, pp. e108438
-
-
Schneider, M.1
Brock, O.2
-
54
-
-
84979849758
-
RBO Aleph: leveraging novel information sources for protein structure prediction
-
Mabrouk M., Putz I., Werner T., Schneider M., Neeb M., Bartels P., Brock O. RBO Aleph: leveraging novel information sources for protein structure prediction. Nucleic Acids Res 2015, 43:W343-W348.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. W343-W348
-
-
Mabrouk, M.1
Putz, I.2
Werner, T.3
Schneider, M.4
Neeb, M.5
Bartels, P.6
Brock, O.7
-
55
-
-
84938421661
-
Protein structure determination by combining sparse NMR data with evolutionary couplings
-
Tang Y., Huang Y.J., Hopf T.A., Sander C., Marks D.S., Montelione G.T. Protein structure determination by combining sparse NMR data with evolutionary couplings. Nat Methods 2015, 12:751-754.
-
(2015)
Nat Methods
, vol.12
, pp. 751-754
-
-
Tang, Y.1
Huang, Y.J.2
Hopf, T.A.3
Sander, C.4
Marks, D.S.5
Montelione, G.T.6
-
56
-
-
0037398428
-
Ran's C-terminal, basic patch and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras and Ran GTPases
-
Neuwald A.F., Kannan N., Poleksic A., Hata N., Liu J.S. Ran's C-terminal, basic patch and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras and Ran GTPases. Genome Res 2003, 13:673-692.
-
(2003)
Genome Res
, vol.13
, pp. 673-692
-
-
Neuwald, A.F.1
Kannan, N.2
Poleksic, A.3
Hata, N.4
Liu, J.S.5
-
57
-
-
80052443044
-
Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms
-
Neuwald A.F. Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms. Stat Appl Genet Mol Biol 2011, 10:36.
-
(2011)
Stat Appl Genet Mol Biol
, vol.10
, pp. 36
-
-
Neuwald, A.F.1
-
58
-
-
84896767741
-
A Bayesian sampler for optimization of protein domain hierarchies
-
Neuwald A.F. A Bayesian sampler for optimization of protein domain hierarchies. J Comput Biol 2014, 21:269-286.
-
(2014)
J Comput Biol
, vol.21
, pp. 269-286
-
-
Neuwald, A.F.1
-
59
-
-
84907704295
-
Protein domain hierarchy Gibbs sampling strategies
-
Neuwald A.F. Protein domain hierarchy Gibbs sampling strategies. Stat Appl Genet Mol Biol 2014, 13:497-517.
-
(2014)
Stat Appl Genet Mol Biol
, vol.13
, pp. 497-517
-
-
Neuwald, A.F.1
-
60
-
-
84862572256
-
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures
-
Neuwald A.F., Lanczycki C.J., Marchler-Bauer A. Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. BMC Bioinf 2012, 13:144.
-
(2012)
BMC Bioinf
, vol.13
, pp. 144
-
-
Neuwald, A.F.1
Lanczycki, C.J.2
Marchler-Bauer, A.3
-
61
-
-
67349190989
-
The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches
-
Neuwald A.F. The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches. J Mol Biol 2009, 390:142-153.
-
(2009)
J Mol Biol
, vol.390
, pp. 142-153
-
-
Neuwald, A.F.1
-
62
-
-
62549113471
-
The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops
-
Neuwald A.F. The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops. BMC Struct Biol 2009, 9:11.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 11
-
-
Neuwald, A.F.1
-
63
-
-
0345492351
-
Allosteric determinants in guanine nucleotide-binding proteins
-
Hatley M.E., Lockless S.W., Gibson S.K., Gilman A.G., Ranganathan R. Allosteric determinants in guanine nucleotide-binding proteins. Proc Natl Acad Sci U S A 2003, 100:14445-14450.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 14445-14450
-
-
Hatley, M.E.1
Lockless, S.W.2
Gibson, S.K.3
Gilman, A.G.4
Ranganathan, R.5
-
64
-
-
84886290642
-
CAFA and the open world of protein function predictions
-
Dessimoz C., Skunca N., Thomas P.D. CAFA and the open world of protein function predictions. Trends Genet 2013, 29:609-610.
-
(2013)
Trends Genet
, vol.29
, pp. 609-610
-
-
Dessimoz, C.1
Skunca, N.2
Thomas, P.D.3
-
65
-
-
84907024436
-
The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective
-
Jiang Y., Clark W.T., Friedberg I., Radivojac P. The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinformatics 2014, 30:i609-i616.
-
(2014)
Bioinformatics
, vol.30
, pp. i609-i616
-
-
Jiang, Y.1
Clark, W.T.2
Friedberg, I.3
Radivojac, P.4
-
66
-
-
84896926969
-
Evaluating, comparing, and interpreting protein domain hierarchies
-
Neuwald A.F. Evaluating, comparing, and interpreting protein domain hierarchies. J Comput Biol 2014, 21:287-302.
-
(2014)
J Comput Biol
, vol.21
, pp. 287-302
-
-
Neuwald, A.F.1
-
67
-
-
40049091146
-
Prediction of protein functional residues from sequence by probability density estimation
-
Fischer J.D., Mayer C.E., Soding J. Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 2008, 24:613-620.
-
(2008)
Bioinformatics
, vol.24
, pp. 613-620
-
-
Fischer, J.D.1
Mayer, C.E.2
Soding, J.3
-
68
-
-
84864886655
-
Structural and biochemical characterization of a trapped coenzyme A adduct of Caenorhabditis elegans glucosamine-6-phosphate N-acetyltransferase 1
-
Dorfmueller H.C., Fang W., Rao F.V., Blair D.E., Attrill H., van Aalten D.M. Structural and biochemical characterization of a trapped coenzyme A adduct of Caenorhabditis elegans glucosamine-6-phosphate N-acetyltransferase 1. Acta Crystallogr D Biol Crystallogr 2012, 68:1019-1029.
-
(2012)
Acta Crystallogr D Biol Crystallogr
, vol.68
, pp. 1019-1029
-
-
Dorfmueller, H.C.1
Fang, W.2
Rao, F.V.3
Blair, D.E.4
Attrill, H.5
van Aalten, D.M.6
-
69
-
-
84966452493
-
Bayesian top-down protein sequence alignment with inferred position-specific gap penalties
-
Neuwald A.F., Altschul S.F. Bayesian top-down protein sequence alignment with inferred position-specific gap penalties. PLoS Comput Biol 2016, 12:e1004936. 10.1371/journal.pcbi.1004936.
-
(2016)
PLoS Comput Biol
, vol.12
, pp. e1004936
-
-
Neuwald, A.F.1
Altschul, S.F.2
-
71
-
-
1642483424
-
The structural GDP/GTP cycle of Rab11 reveals a novel interface involved in the dynamics of recycling endosomes
-
Pasqualato S., Senic-Matuglia F., Renault L., Goud B., Salamero J., Cherfils J. The structural GDP/GTP cycle of Rab11 reveals a novel interface involved in the dynamics of recycling endosomes. J Biol Chem 2004, 279:11480-11488.
-
(2004)
J Biol Chem
, vol.279
, pp. 11480-11488
-
-
Pasqualato, S.1
Senic-Matuglia, F.2
Renault, L.3
Goud, B.4
Salamero, J.5
Cherfils, J.6
|