A comparison of position-specific score matrices based on sequence and structure alignments

Protein Science

Volumn 11, Issue 2, 2002, Pages 361-370

  Panchenko, Anna R ^a   Bryant, Stephen H ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Alignment accuracy; Profile search; Protein structure alignment

Indexed keywords

PROTEIN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN STRUCTURE; SCORING SYSTEM; STRUCTURE ANALYSIS;

ALGORITHMS; DATABASES, FACTUAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY; SOFTWARE;

EID: 0036145804     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.19902     Document Type: Article

References (37)

1. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
2. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
3. The Protein Data Bank and the challenge of structural genomics
4. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
5. The relation between the divergence of sequence and structure in proteins
6. Hidden Markov models
7. Comparison of conformational characteristics in structurally similar protein pairs
8. Surprising similarities in structure comparison
9. Profile analysis: Detection of distantly related proteins
10. Unification of protein families
11. Parser for protein folding units
12. Comparison of solvent-inaccessible cores of homologous proteins: Definitions useful for protein modelling
13. Hidden Markov models for sequence analysis: Extension and analysis of the basic method
14. Predicting protein structure using hidden Markov models
15. Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM
16. Enhanced genome annotation using structural profiles in the program 3D-PSSM
17. Threading a database of protein cores
18. MMDB: Entrez's 3D structure database
19. Measures of threading specificity and accuracy
20. Identification of homologous core structures
21. Critical assessment of methods of protein structure prediction (CASP): Round II
22. How far divergent evolution goes in proteins
23. SCOP: A structural classification of proteins database for the investigation of sequences and structures
24. Extracting protein alignment models from the sequence database
25. T-Coffee: A novel method for fast and accurate multiple sequence alignment
26. Combination of threading potentials and sequence profiles improves fold recognition
27. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
28. A protein taxonomy based on secondary structure
29. Protein structures sustain evolutionary drift
30. Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility
31. Comparison of sequence profiles. Strategies for structural predictions using sequence information
32. Genome analysis: Assigning protein coding regions to three-dimensional structures
33. Large-scale comparison of protein sequence alignment algorithms with structure alignments
34. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
35. A comprehensive comparison of multiple sequence alignment programs
36. Evolution of protein sequences and structures