Identification of functionally conserved residues with the use of entropy-variability plots.

by: L Oliveira, PB Paiva, AC Paiva, G Vriend

Proteins, Vol. 52, No. 4. (1 September 2003), pp. 544-552.

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Abstract

We introduce sequence entropy-variability plots as a method of analyzing families of protein sequences, and demonstrate this for three well-known sequence families: globins, ras-like proteins, and serine-proteases. The location of an aligned residue position in the entropy-variability plot correlates with structural characteristics, and with known facts about the roles of individual amino acids in the function of these proteins. The large numbers of known sequences in these families allowed us to introduce new filtering methods for variability patterns. The results are discussed in terms of a simple evolutionary model for functional proteins.

@article{citeulike:271228, abstract = {We introduce sequence entropy-variability plots as a method of analyzing families of protein sequences, and demonstrate this for three well-known sequence families: globins, ras-like proteins, and serine-proteases. The location of an aligned residue position in the entropy-variability plot correlates with structural characteristics, and with known facts about the roles of individual amino acids in the function of these proteins. The large numbers of known sequences in these families allowed us to introduce new filtering methods for variability patterns. The results are discussed in terms of a simple evolutionary model for functional proteins.}, address = {Escola Paulista de Medicina, Universidade Federal de S\~{a}o Paulo, S\~{a}o Paulo, Brazil.}, author = {Oliveira, L. and Paiva, P. B. and Paiva, A. C. and Vriend, G. }, citeulike-article-id = {271228}, doi = {10.1002/prot.10490}, issn = {1097-0134}, journal = {Proteins}, keywords = {bioinformatics, protein\_design, protein\_sequence, sequence\_comparison}, month = {September}, number = {4}, pages = {544--552}, posted-at = {2005-08-01 22:41:32}, priority = {2}, title = {Identification of functionally conserved residues with the use of entropy-variability plots.}, url = {http://dx.doi.org/10.1002/prot.10490}, volume = {52}, year = {2003} }

RIS record

TY - JOUR ID - citeulike:271228 L3 - citeulike-article-id:271228 TI - Identification of functionally conserved residues with the use of entropy-variability plots. JF - Proteins VL - 52 IS - 4 SP - 544 EP - 552 AD - Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil. SN - 1097-0134 N2 - We introduce sequence entropy-variability plots as a method of analyzing families of protein sequences, and demonstrate this for three well-known sequence families: globins, ras-like proteins, and serine-proteases. The location of an aligned residue position in the entropy-variability plot correlates with structural characteristics, and with known facts about the roles of individual amino acids in the function of these proteins. The large numbers of known sequences in these families allowed us to introduce new filtering methods for variability patterns. The results are discussed in terms of a simple evolutionary model for functional proteins. KW - bioinformatics KW - protein_design KW - protein_sequence KW - sequence_comparison AU - Oliveira, L AU - Paiva, PB AU - Paiva, AC AU - Vriend, G PY - 2003/09/01/ UR - http://dx.doi.org/10.1002/prot.10490 ER -

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