Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations [4]

Molecular Biology and Evolution

Volumn 19, Issue 3, 2002, Pages 352-356

  Fornasari, María Silvina ^a   Parisi, Gustavo ^a   Echave, Julian ^a  

^a UNIVERSIDAD NACIONAL DE QUILMES   (Argentina)

Author keywords

Model; Molecular evolution; Protein evolution; Simulation; Substitution matrix

Indexed keywords

AMINO ACID;

AMINO ACID SUBSTITUTION; LETTER; MOLECULAR EVOLUTION; MOLECULAR MODEL; NONHUMAN; PROTEIN STRUCTURE; SIMULATION; SITE DIRECTED MUTAGENESIS; SWISS-PROT;

EID: 0036184351     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004089     Document Type: Letter

References (25)

1. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
2. Construction of phylogenetic trees
3. Statistical tests of models of DNA substitution
4. Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
5. The rapid generation of mutation data matrices from protein sequences
6. Context-dependent optimal substitution matrices
7. Models of natural mutations including site heterogeneity
8. Models of molecular evolution and phylogeny
9. PASSML: Combining evolutionary inference and protein secondary structure prediction
10. Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
11. Structural constraints and emergence of sequence patterns in protein evolution
12. The effect of branch length variation on the selection of models of molecular evolution
13. A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase
14. Estimating the dimension of a model
15. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
16. Models of protein sequence evolution and their applications
17. Combining protein evolution and secondary structure
18. Eight bacterial proteins, including UDP-N-acetylglucosamine acyltransferase (LpxA) and three other transferases of Escherichia coli, consist of a six-residue periodicity theme
19. The novel hexapeptide motif found in the acyltransferases LpxA and LpxD of lipid A biosynthesis is conserved in various bacteria
20. Molecular phylogenetics: State-of-the-art methods for looking into the past
21. The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase, chemical modification and site-directed mutagenesis
22. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
23. PAML: A program package for phylogenetic analysis by maximum likelihood
24. Models of amino acid substitution and applications to mitochondrial protein evolution