Scoring residue conservation

Proteins: Structure, Function and Genetics

Volumn 48, Issue 2, 2002, Pages 227-241

  Valdar, William S J ^a,b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Amino acid; Evolutionary conservation; Multiple sequence alignment; Protein sequence analysis; Variability

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ENTROPY; GENE MUTATION; GENETIC CONSERVATION; GENETIC VARIABILITY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE ANALYSIS; STEREOCHEMISTRY;

AMINO ACIDS; CONSERVED SEQUENCE; ENTROPY; EVOLUTION, MOLECULAR; MUTATION; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STEREOISOMERISM;

EID: 0036681416     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10146     Document Type: Article

References (50)

1. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
2. Hidden markov models
3. An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity
4. Information-theoretical entropy as a measure of sequence variability
5. Resolution of hypervariable regions in T-cell receptor β chains by a modified Wu-Kabat index of amino acid diversity
6. Evolutionarily conserved pathways of energetic connectivity in protein families
7. A mathematical theory of communication
8. Properties of a generalized diversity index
9. The population frequencies of species and the estimation of population parameters
10. Information content of individual genetic sequences
11. Database of homology-derived protein structures and the structural meaning of sequence alignment
12. Average core structures and variability measures for protein families: Application to the immunoglobulins
13. Evolutionary conservation of the folding nucleus
14. Evolutionary conservation in protein folding kinetics
15. The classification of amino acid conservation
16. A model of evolutionary change in proteins: Matrices for detecting distant relationships
17. Prediction of protein secondary structure and active sites using the alignment of homologous sequences
18. Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
19. Hidden Markov models for sequence analysis: Extension and analysis of the basic method
20. Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology
21. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
22. Evolutionary conservation of RecA genes in relation to protein structure and function
23. Amino acid substitution matrices from protein blocks
24. ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
25. An evolutionary trace method defines binding surfaces common to protein families
26. Two types of amino acid substitutions in protein evolution
27. The CLUSTALX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
28. Using CLUSTAL for multiple sequence alignments
29. The variable and conserved interfaces of modeled olfactory receptor proteins
30. Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
31. Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters
32. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling
33. A fast and sensitive multiple sequence alignment algorithm
34. Weighting hidden Markov models for maximum discrimination
35. Position-based sequence weights
36. PSIC: Profile extraction from sequence alignments with position-specific counts of independent observations
37. Optimal classification of protein sequences and selection of representative sets from multiple alignments: Application to homologous families and lessons for structural genomics
38. Equal animals
39. Volume changes in protein evolution
40. Weights for data related by a tree
41. Maximum discrimination hidden Markov models of sequence consensus
42. Analysis of heregulin symmetry by weighted evolutionary tracing
43. Amino acid substitution during functionally constrained divergent evolution of protein sequences
44. Protein-protein interfaces: Analysis of amino acid conservation in homodimers
45. The rapid generation of mutation data matrices from protein sequences
46. Weighting aligned protein or nucleic acid sequences to correct for unequal representation
47. Accurate formula for P-values of gapped local sequence and profile alignments