-
1
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Gobel, U., Sander, C., Scheider, R., et al. (1994) Correlated mutations and residue contacts in proteins. Proteins 18, 309-317.
-
(1994)
Proteins
, vol.18
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Scheider, R.3
-
2
-
-
0015243774
-
Tests for comparing related amino acid sequences
-
McLachlan, A.D. (1971) Tests for comparing related amino acid sequences. J Mol Biol 61, 409-424.
-
(1971)
J Mol Biol
, vol.61
, pp. 409-424
-
-
McLachlan, A.D.1
-
3
-
-
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(1), 98-102.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, Issue.1
, pp. 98-102
-
-
Neher, E.1
-
4
-
-
13944252115
-
Prediction of distant residue contacts with the use of evolutionary information
-
Vicatos, S., Reddy, B.V.B., and Kaznessis, Y. (2005) Prediction of distant residue contacts with the use of evolutionary information. Proteins: Structure, Function, and Bioinformatics 58, 935-949.
-
(2005)
Proteins: Structure, Function, and Bioinformatics
, vol.58
, pp. 935-949
-
-
Vicatos, S.1
Reddy, B.V.B.2
Kaznessis, Y.3
-
5
-
-
0036763251
-
Prediction of protein residue contacts with a PDB-derived likelihood matrix
-
Singer, M.S., Vriend, G., and Bywater, R.P. (2002) Prediction of protein residue contacts with a PDB-derived likelihood matrix. Protein Eng 15(9), 721-725.
-
(2002)
Protein Eng
, vol.15
, Issue.9
, pp. 721-725
-
-
Singer, M.S.1
Vriend, G.2
Bywater, R.P.3
-
6
-
-
0038010382
-
Testing homology with CAO: A contact-based Markov model of protein evolution
-
Lin, K., Kleinjung, J., Taylor, W., et al. (2003) Testing homology with CAO: A contact-based Markov model of protein evolution. Comp Biol Chem 27, 93-102.
-
(2003)
Comp Biol Chem
, vol.27
, pp. 93-102
-
-
Lin, K.1
Kleinjung, J.2
Taylor, W.3
-
7
-
-
0028832687
-
Covariation of residues in the homeodomain sequence family
-
Clarke, N.D. (1995) Covariation of residues in the homeodomain sequence family. Protein Sci. 7(11), 2269-78.
-
(1995)
Protein Sci
, vol.7
, Issue.11
, pp. 2269-2278
-
-
Clarke, N.D.1
-
8
-
-
0027297096
-
Covariation of Mutations in the V3 Loop of Human Immunodeficiency Virus Type 1 Envelope Protein: An Information Theoretic Analysis
-
Korber, B.T.M., Farber, R.M., Wolpert, D.H., et al. (1993) Covariation of Mutations in the V3 Loop of Human Immunodeficiency Virus Type 1 Envelope Protein: An Information Theoretic Analysis. Proc Natl Acad Sci 90, 7176-7180.
-
(1993)
Proc Natl Acad Sci
, vol.90
, pp. 7176-7180
-
-
Korber, B.T.M.1
Farber, R.M.2
Wolpert, D.H.3
-
9
-
-
27944458910
-
Using information theory to search for co-evolving residues in proteins
-
Martin, L.C., Gloor, G.B., Dunn, S.D., et al. (2005) Using information theory to search for co-evolving residues in proteins. Bioinformatics 21(22), 4116-4124.
-
(2005)
Bioinformatics
, vol.21
, Issue.22
, pp. 4116-4124
-
-
Martin, L.C.1
Gloor, G.B.2
Dunn, S.D.3
-
10
-
-
0037020282
-
Correlated Mutation Analyses on Very Large Sequence Families
-
Oliveira, L., Paiva, A.C.M., and Vriend, G. (2002) Correlated Mutation Analyses on Very Large Sequence Families. Chem Bio Chem 3(10), 1010-1017.
-
(2002)
Chem Bio Chem
, vol.3
, Issue.10
, pp. 1010-1017
-
-
Oliveira, L.1
Paiva, A.C.M.2
Vriend, G.3
-
11
-
-
0033832578
-
Phylogenetically enhanced statistical tools for RNA structure prediction
-
Akmaev, V.R., Kelley, S.T., and Stormo, G.D. (2000) Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinformatics 16(6), 501-512.
-
(2000)
Bioinformatics
, vol.16
, Issue.6
, pp. 501-512
-
-
Akmaev, V.R.1
Kelley, S.T.2
Stormo, G.D.3
-
12
-
-
0037433701
-
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
-
Tillier, E.R.M. and Lui, T.W.H. (2003) Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics 19(6), 750-755.
-
(2003)
Bioinformatics
, vol.19
, Issue.6
, pp. 750-755
-
-
Tillier, E.R.M.1
Lui, T.W.H.2
-
13
-
-
0034724418
-
Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap
-
Wollenberg, K.R., and Atchley, W.R. (2000) Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc Natl Acad Sci USA 97, 3288-3291.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 3288-3291
-
-
Wollenberg, K.R.1
Atchley, W.R.2
-
14
-
-
0034044314
-
The PSIPRED protein structure prediction server
-
McGuffin, L.J., Bryson, K., and Jones, D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics 16, 404-405.
-
(2000)
Bioinformatics
, vol.16
, pp. 404-405
-
-
McGuffin, L.J.1
Bryson, K.2
Jones, D.T.3
-
17
-
-
0003421109
-
-
University of Stuttgart
-
Zell, A., Marnier, M., Vogt, N., et al, Stuttgart Neural Network Simulator User Manual Version 4.2. 1998: University of Stuttgart.
-
(1998)
Stuttgart Neural Network Simulator User Manual Version 4.2
-
-
Zell, A.1
Marnier, M.2
Vogt, N.3
-
18
-
-
21444454088
-
PROFcon: Novel prediction of long range contacts
-
Punta, M., and Rost, B. (2005) PROFcon: novel prediction of long range contacts. Bioinformatics 21(13), 2960-2968.
-
(2005)
Bioinformatics
, vol.21
, Issue.13
, pp. 2960-2968
-
-
Punta, M.1
Rost, B.2
-
19
-
-
4043170491
-
Protein contact prediction using patterns of correlation
-
Hamilton, N., Burrage, K., Ragan, M.A., et al. (2004) Protein contact prediction using patterns of correlation. Proteins: Structure, Function, and Bioinformatics 56, 679-684.
-
(2004)
Proteins: Structure, Function, and Bioinformatics
, vol.56
, pp. 679-684
-
-
Hamilton, N.1
Burrage, K.2
Ragan, M.A.3
-
20
-
-
0035663988
-
Prediction of contact maps with neural networks and correlated mutations
-
Fariselli, P., Olmea, O., Valencia, A., et al. (2001) Prediction of contact maps with neural networks and correlated mutations. Protein Eng 14, 835-843.
-
(2001)
Protein Eng
, vol.14
, pp. 835-843
-
-
Fariselli, P.1
Olmea, O.2
Valencia, A.3
-
21
-
-
24744453057
-
Stripped sheets and protein contact prediction
-
MacCallum, R.M. (2004) Stripped sheets and protein contact prediction. Bioinformatics 20(1), i224-i231.
-
(2004)
Bioinformatics
, vol.20
, Issue.1
-
-
MacCallum, R.M.1
-
24
-
-
85069247670
-
-
Chang, C-C, and Lin, C-J, LIBSVM: a library for support vector machines. Software available at http://www.csie.ntu.edu. tw/ cjlin/libsvm. 2001.
-
Chang, C-C, and Lin, C-J, LIBSVM: a library for support vector machines. Software available at http://www.csie.ntu.edu. tw/ cjlin/libsvm. 2001.
-
-
-
-
26
-
-
0242362161
-
Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction
-
Karplus, K., Karchin, R., Draper, J., et al. (2003) Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins: Structure, Function, and Genetics 53(S6), 491-496.
-
(2003)
Proteins: Structure, Function, and Genetics
, vol.53
, Issue.S6
, pp. 491-496
-
-
Karplus, K.1
Karchin, R.2
Draper, J.3
-
27
-
-
0042721397
-
Predicting Interresidue contacts using templates and pathways
-
Shao, Y. and Bystroff, C. (2003) Predicting Interresidue contacts using templates and pathways. Proteins 53, 497-502.
-
(2003)
Proteins
, vol.53
, pp. 497-502
-
-
Shao, Y.1
Bystroff, C.2
-
28
-
-
3042565868
-
Automatic Identification of Subcellular Phenotypes on Human Cell Arrays
-
Conrad, C., Erfle, H., Warnat, P., et al. (2004) Automatic Identification of Subcellular Phenotypes on Human Cell Arrays. Genome Research 14, 1130-1136.
-
(2004)
Genome Research
, vol.14
, pp. 1130-1136
-
-
Conrad, C.1
Erfle, H.2
Warnat, P.3
-
29
-
-
28944438120
-
Improving disulphide connectivity prediction with sequential distance between oxidized cysteines
-
Tsai, C-H, Chen, B-J, Chan, C-h, et al. (2005) Improving disulphide connectivity prediction with sequential distance between oxidized cysteines. Bioinformatics 21(4), 4416-4419.
-
(2005)
Bioinformatics
, vol.21
, Issue.4
, pp. 4416-4419
-
-
Tsai, C.-H.1
Chen, B.-J.2
Chan, C.-H.3
-
30
-
-
85069256756
-
-
Hu, J., Shen, X., Shao, Y., et al., eds. Mining protein contact maps. In 2nd BIOKDD Workshop on Data Mining in Bioinformatics. 2002.
-
Hu, J., Shen, X., Shao, Y., et al., eds. Mining protein contact maps. In 2nd BIOKDD Workshop on Data Mining in Bioinformatics. 2002.
-
-
-
-
31
-
-
27644490770
-
Better prediction of protein contact number using a support vector regression analysis if amino acid sequence
-
Yuan, Z. (2005) Better prediction of protein contact number using a support vector regression analysis if amino acid sequence. BMC Bioinformatics 6, 248-257.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 248-257
-
-
Yuan, Z.1
-
32
-
-
0242299187
-
Predictions without templates: New folds, secondary structure, and contacts in CASP5
-
Aloy, P., Stark, A., Hadley, C., et al. (2003) Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins Suppl. 6, 436-456.
-
(2003)
Proteins Suppl
, vol.6
, pp. 436-456
-
-
Aloy, P.1
Stark, A.2
Hadley, C.3
-
33
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
Olmea, O., and Valencia, A. (1997) Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Design 2, S25-S32.
-
(1997)
Fold Design
, vol.2
-
-
Olmea, O.1
Valencia, A.2
-
34
-
-
0030443368
-
Protein Fold Recognition and Dynamics in The Space of Contact Maps
-
Mirny, L. and Domany, E. (1996) Protein Fold Recognition and Dynamics in The Space of Contact Maps. Proteins 26, 319-410.
-
(1996)
Proteins
, vol.26
, pp. 319-410
-
-
Mirny, L.1
Domany, E.2
-
35
-
-
0035700864
-
Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations
-
Fariselli, P., Olmea, O., Valencia, A., et al. (2001) Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins Suppl 5, 157-162.
-
(2001)
Proteins Suppl
, vol.5
, pp. 157-162
-
-
Fariselli, P.1
Olmea, O.2
Valencia, A.3
-
36
-
-
0033047710
-
Neural network based prediction of residue contacts in protein
-
Fariselli, P. and Casadio, R. (1999) Neural network based prediction of residue contacts in protein. Protein Eng 12, 15-21.
-
(1999)
Protein Eng
, vol.12
, pp. 15-21
-
-
Fariselli, P.1
Casadio, R.2
-
37
-
-
30344453347
-
CASP6 assessment of contact prediction
-
Gran̈a, O., Baker, D., Maccallum, R.M., et al. (2005) CASP6 assessment of contact prediction. Proteins: Structure, Function, and Bioinformatics 61 Suppl 7, 214-24.
-
(2005)
Proteins: Structure, Function, and Bioinformatics 61
, Issue.SUPPL. 7
, pp. 214-224
-
-
Gran̈a, O.1
Baker, D.2
Maccallum, R.M.3
-
38
-
-
0043123211
-
EVA: Evaluation of protein structure prediction servers
-
Koh, I.Y.Y., Eyrich, V.A., Marti-Renom, M.A., et al. (2003) EVA: evaluation of protein structure prediction servers. Nucleic Acids Research 31, 3311-3315.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3311-3315
-
-
Koh, I.Y.Y.1
Eyrich, V.A.2
Marti-Renom, M.A.3
-
39
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos, F., Helmer-Citterich, M., and Ausiello, G. (1997) Correlated mutations contain information about protein-protein interaction. J Mol Biol 271, 511-523.
-
(1997)
J Mol Biol
, vol.271
, pp. 511-523
-
-
Pazos, F.1
Helmer-Citterich, M.2
Ausiello, G.3
-
40
-
-
11144241105
-
LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
-
Rychlewski, L., and Fischer, D. (2005) LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction. Protein Science 14, 240-245.
-
(2005)
Protein Science
, vol.14
, pp. 240-245
-
-
Rychlewski, L.1
Fischer, D.2
-
41
-
-
0041719954
-
Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
-
Pollastri, G. and Baldi, P. (2002) Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics 18(Suppl. 1), S62-S70.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Pollastri, G.1
Baldi, P.2
-
42
-
-
24744471870
-
The self-organizing feature maps
-
Kohonen, T., and Makisari, K. (1989) The self-organizing feature maps. Phys Scripta 39, 168-172.
-
(1989)
Phys Scripta
, vol.39
, pp. 168-172
-
-
Kohonen, T.1
Makisari, K.2
-
43
-
-
0346494941
-
SCOP database in 2004: Refinements integrate structure and sequence family data
-
Database issue, D226-9
-
Andreeva, A., Howorth, D., Brenner, S.E., et al. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research 32(Database issue), D226-9.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
-
44
-
-
30344488120
-
TASSER: An automated method for the prediction of protein tertiary structures. Proteins: Structure, Function, and Bioinformatics
-
Zhang, Y., Arakaki, A.K., and Skolnick, J. (2005) TASSER: An automated method for the prediction of protein tertiary structures. Proteins: Structure, Function, and Bioinformatics Suppl. 7, 91-98.
-
(2005)
Suppl
, vol.7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
-
45
-
-
3242887695
-
Protein structure prediction and analysis using the Robetta server
-
Kim, D.E., Chivian, D., and Baker, D. (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research 32, W526-W531.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Kim, D.E.1
Chivian, D.2
Baker, D.3
|