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Literature DB >> 15215352

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.

Dmitry A Afonnikov¹, Nikolay A Kolchanov.

Abstract

Recent results suggest that during evolution certain substitutions at protein sites may occur in a coordinated manner due to interactions between amino acid residues. Information on these coordinated substitutions may be useful for analysis of protein structure and function. CRASP is an Internet-available software tool for the detection and analysis of coordinated substitutions in multiple alignments of protein sequences. The approach is based on estimation of the correlation coefficient between the values of a physicochemical parameter at a pair of positions of sequence alignment. The program enables the user to detect and analyze pairwise relationships between amino acid substitutions at protein sequence positions, estimate the contribution of the coordinated substitutions to the evolutionary invariance or variability in integral protein physicochemical characteristics such as the net charge of protein residues and hydrophobic core volume. The CRASP program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/.

Mesh：

Year: 2004 PMID： 15215352 PMCID： PMC441589 DOI： 10.1093/nar/gkh451

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

30 in total

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Authors: D A Afonnikov; D Y Oshchepkov; N A Kolchanov
Journal: Bioinformatics Date: 2001-11 Impact factor: 6.937

2. Can correlated mutations in protein domain families be used for protein design?

Authors: S B Nagl
Journal: Brief Bioinform Date: 2001-09 Impact factor: 11.622

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Authors: M Kimura
Journal: Proc Natl Acad Sci U S A Date: 1991-07-15 Impact factor: 11.205

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Authors: T Vernet; D C Tessier; H E Khouri; D Altschuh
Journal: J Mol Biol Date: 1992-03-20 Impact factor: 5.469

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Authors: S A Benner; D Gerloff
Journal: Adv Enzyme Regul Date: 1991

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Authors: M Vingron; P Argos
Journal: Comput Appl Biosci Date: 1989-04

7. Bona fide prediction of aspects of protein conformation. Assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences.

Authors: S A Benner; I Badcoe; M A Cohen; D L Gerloff
Journal: J Mol Biol Date: 1994-01-21 Impact factor: 5.469

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.

1. Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions.

2. Can correlated mutations in protein domain families be used for protein design?

3. Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics.

4. Correlation of co-ordinated amino acid changes at the two-domain interface of cysteine proteases with protein stability.

Review 5. 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.

6. A fast and sensitive multiple sequence alignment algorithm.

7. Bona fide prediction of aspects of protein conformation. Assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences.

8. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

9. Volume changes in protein evolution.

10. The helical hydrophobic moment: a measure of the amphiphilicity of a helix.

1. Evolutionary analysis of phycobiliproteins: implications for their structural and functional relationships.

2. Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain.

3. UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB.

4. Amino acid sequence coevolution in the insect bursicon ligand-receptor system.

5. Fuzzy clustering of physicochemical and biochemical properties of amino acids.

6. Coordinated evolution of the hepatitis C virus.

7. Janus: prediction and ranking of mutations required for functional interconversion of enzymes.

8. Conserved and variable correlated mutations in the plant MADS protein network.

9. Hyperdimensional analysis of amino acid pair distributions in proteins.

10. Correlated mutations via regularized multinomial regression.