Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences.
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S A Benner | S. Benner | K. Fukami-Kobayashi | D. Schreiber | K Fukami-Kobayashi | D R Schreiber | Kaoru Fukami-Kobayashi | David R Schreiber | S. A. Benner
[1] E. Neher. How frequent are correlated changes in families of protein sequences? , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[2] G Chelvanayagam,et al. A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure. , 1998, Folding & design.
[3] M. O. Dayhoff,et al. Atlas of protein sequence and structure , 1965 .
[4] C. Sander,et al. Correlated mutations and residue contacts in proteins , 1994, Proteins.
[5] Chantal Roth-Korostensky,et al. Algorithms for building multiple sequence alignments and evolutionary trees , 2000 .
[6] S. Benner. Reconstructing the Evolution of Proteins , 1988 .
[7] W. Messier,et al. Episodic adaptive evolution of primate lysozymes , 1997, Nature.
[8] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[9] C. Luo,et al. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. , 1985, Molecular biology and evolution.
[10] M. Nei,et al. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. , 2000, Molecular biology and evolution.
[11] A. Bairoch,et al. The SWISS-PROT protein sequence data bank. , 1991, Nucleic acids research.
[12] G. Chelvanayagam,et al. An analysis of simultaneous variation in protein structures. , 1997, Protein engineering.
[13] S. Benner,et al. Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics. , 2000, Research in microbiology.
[14] J. Felsenstein,et al. Inching toward reality: An improved likelihood model of sequence evolution , 2004, Journal of Molecular Evolution.
[15] Burkhard Rost,et al. PHD - an automatic mail server for protein secondary structure prediction , 1994, Comput. Appl. Biosci..
[16] Redesigning the Molecules of Life , 1988, Springer Berlin Heidelberg.
[17] M. Gerstein,et al. Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins , 2001, Genome Research.
[18] W. Fitch. Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .
[19] Scott R. Presnell,et al. The ribonuclease from an extinct bovid ruminant , 1990, FEBS letters.
[20] K. Holsinger. The neutral theory of molecular evolution , 2004 .
[21] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[22] K. Hatrick,et al. Compensating changes in protein multiple sequence alignments. , 1994, Protein engineering.
[23] Gaston H. Gonnet,et al. Computational biochemistry research at ETH , 1991 .
[24] S. Benner,et al. Post-genomic science: converting primary structure into physiological function. , 1998, Advances in enzyme regulation.
[25] G. Gonnet,et al. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. , 1993, Journal of molecular biology.
[26] U. Hobohm,et al. Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.
[27] M. Miyamoto,et al. Testing the covarion hypothesis of molecular evolution. , 1995, Molecular biology and evolution.
[28] S. Benner,et al. Interpreting the behavior of enzymes: purpose or pedigree? , 1988, CRC critical reviews in biochemistry.
[29] M M Miyamoto,et al. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[30] S. Benner,et al. Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. , 1991, Advances in enzyme regulation.
[31] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[32] Brian W. Matthews,et al. Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing , 1990, Nature.
[33] A. Lesk,et al. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. , 1987, Journal of molecular biology.
[34] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[35] F. Cohen,et al. Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.
[36] David A Liberles,et al. The Adaptive Evolution Database (TAED) , 2001, Genome Biology.
[37] B. Rost,et al. Effective use of sequence correlation and conservation in fold recognition. , 1999, Journal of molecular biology.
[38] Marcel Turcotte,et al. Bona Fide Predictions of Protein Secondary Structure Using Transparent Analyses of Multiple Sequence Alignments , 1998 .
[39] S A Benner,et al. Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix. , 1994, Biochemical and biophysical research communications.
[40] J. Huelsenbeck,et al. Application and accuracy of molecular phylogenies. , 1994, Science.
[41] C. Sander,et al. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? , 1994, Protein engineering.
[42] M. Sternberg,et al. Modelling the ATP‐binding site of oncogene products, the epidermal growth factor receptor and related proteins , 1984, FEBS letters.
[43] J. Skolnick,et al. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. , 1998, Journal of molecular biology.
[44] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[45] Steven A. Benner,et al. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily , 1995, Nature.
[46] K. Nagai,et al. Coordinated amino acid changes in homologous protein families. , 1988, Protein engineering.
[47] S. Benner,et al. Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function? , 1996, FEBS letters.