Amino acid similarity matrices based on force fields

Bioinformatics

Volumn 17, Issue 8, 2001, Pages 686-699

  Dosztaányi, Zsuzsanna ^a   Torda, Andrew E ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; ENERGY; MATHEMATICAL COMPUTING; METHODOLOGY; MUTATION; PHILOSOPHY; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE ANALYSIS;

EID: 0034855724     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.8.686     Document Type: Article

References (44)

1. A protein alignment scoring system sensitive at all evolutionary distances
2. Hierarchy of regions of amino acid sequence with respect to their role in the protein spatial structure
3. Pairwise sequence alignment below the twilight zone
4. A model of evolutionary change in proteins. Matrices for detecting distant relationships
5. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy
6. Aligning amino acid sequences: Comparison of commonly used methods
7. Optimum superimposition of protein structures: Ambiguities and implications
8. An improved method of testing for evolutionary homology
9. Mutation data matrix and its uses
10. Exhaustive matching of the entire protein sequence database
11. An improved algorithm for matching biological sequences
12. Amino acid difference formula to help explain protein evolution
13. Amino acid substitution matrices from protein blocks
14. Enlarged representative set of protein structures
15. Dictionary of recurrent domains in protein structures
16. Sausage: Protein threading with flexible force fields
17. Protein fold recognition without Boltzmann statistics or explicit physical basis
18. A structural basis for sequence comparisons. An evaluation of scoring methodologies
19. A new approach to protein fold recognition
20. The rapid generation of mutation data matrices from protein sequences
21. Optimization of a new score function for the detection of remote homologs
22. AAindex: Amino acid index database
23. An algorithm for secondary structure determination in proteins based on sequence similarity
24. Towards more meaningful hierarchical classification of amino acid scoring matrices
25. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c551
26. Two types of amino acid substitutions in protein evolution
27. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures
28. New scoring matrix for amino acid residue exchanges based on residue characteristic physical parameters
29. SCOP: A structural classification of proteins database for the investigation of sequences and structures
30. Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles
31. Radial locations of amino acid residues in a globular protein: Correlation with the sequence
32. Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
33. Structure-derived substitution matrices for alignment of distantly related sequences
34. Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix
35. Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
36. Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation
37. Comparison of sequence profiles. Strategies for structural predictions using sequence information
38. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
39. Predicting isomorphic residue replacements for protein design
40. An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zonerevisited
41. Position-dependent protein mutant profile based on mean force field calculation