scholarly journals Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families

2014 ◽  
Vol 23 (9) ◽  
pp. 1220-1234 ◽  
Author(s):  
Jimin Pei ◽  
Wenlin Li ◽  
Lisa N. Kinch ◽  
Nick V. Grishin
Keyword(s):  
Protein Families ◽  
Homologous Protein ◽  
Copper Oxidase ◽  
Evolutionary Units

Coordinated amino acid changes in homologous protein families

1988 ◽  
Vol 2 (3) ◽  
pp. 193-199 ◽  
Author(s):  
D. Altschuh ◽  
T. Vernet ◽  
P. Berti ◽  
D. Moras ◽  
K. Nagai
Keyword(s):  
Amino Acid ◽  
Protein Families ◽  
Homologous Protein

scholarly journals HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families

2001 ◽  
Vol 17 (8) ◽  
pp. 748-749 ◽  
Author(s):  
P. I. W. de Bakker ◽  
A. Bateman ◽  
D. F. Burke ◽  
R. N. Miguel ◽  
K. Mizuguchi ◽  
...  
Keyword(s):  
Sequence Information ◽  
Protein Families ◽  
Homologous Protein

scholarly journals Direct coevolutionary couplings reflect biophysical residue interactions in proteins

2016 ◽  
Author(s):  
Alice Coucke ◽  
Guido Uguzzoni ◽  
Francesco Oteri ◽  
Simona Cocco ◽  
Remi Monasson ◽  
...  
Keyword(s):  
Structural Information ◽  
Synthetic Data ◽  
Chemical Properties ◽  
Quantitative Information ◽  
Protein Families ◽  
Homologous Proteins ◽  
Homologous Protein ◽  
Residue Contact ◽  
Physico Chemical ◽  
Statistical Coupling

AbstractCoevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21×21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices.

scholarly journals Evaluation and improvements of clustering algorithms for detecting remote homologous protein families

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Juliana S Bernardes ◽  
Fabio RJ Vieira ◽  
Lygia MM Costa ◽  
Gerson Zaverucha
Keyword(s):  
Clustering Algorithms ◽  
Protein Families ◽  
Homologous Protein

scholarly journals COGcollator: a web server for analysis of distant relationships between homologous protein families

2017 ◽  
Vol 12 (1) ◽  
Author(s):  
Daria V. Dibrova ◽  
Kirill A. Konovalov ◽  
Vadim V. Perekhvatov ◽  
Konstantin V. Skulachev ◽  
Armen Y. Mulkidjanian
Keyword(s):  
Web Server ◽  
Protein Families ◽  
Homologous Protein
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