Comparison of sequence and structure alignments for protein domains

Proteins: Structure, Function and Genetics

Volumn 48, Issue 3, 2002, Pages 439-446

  Marchler Bauer, Aron ^a   Panchenko, Anna R ^a   Ariel, Naomi ^a   Bryant, Stephen H ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Conserved domain database; Protein domain identification; Sequence alignment; Structure alignment

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DATA BASE; HUMAN; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; THREE DIMENSIONAL IMAGING;

ANIMALS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0037103044     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10163     Document Type: Article

References (47)

1. The multiplicity of domains in proteins
2. The InterPro database, an integrated documentation resource for protein families, domains and functional sites
3. CDD A database of donserved domain alignments with links to domain three-dimensional structure
4. Maximum discrimination hidden Markov models of sequence consensus
5. Hidden Markov models for detecting remote protein homologies
6. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
7. The ProDom database of protein domain families
8. Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities
9. SMART a simple modular architecture research tool: Identification of signaling domains
10. Pfam: A comprehensive database of protein domain families based on seed alignments
11. ProtoMap: Automatic classification of protein sequences and hierarchy of protein families
12. The SYSTERS protein sequence cluster set
13. Methodologies for target selection in structural genomics
14. 3Dee: A database of protein structural domains
15. SCOP. A structural classification of proteins database for the investigation of sequences and structures
16. CATH - A hierarchic classification of protein domain structures
17. MMDB Entrez's 3D structure database
18. The FSSP database of structurally aligned protein fold families
19. A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm
20. Surprising similarities in structure comparison
21. Protein structural domains: Analysis of the 3Dee domains database
22. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP
23. Competitive assessment of protein fold recognition and alignment accuracy
24. Identification of homologous core structures
25. A protein taxonomy based on secondary structure
26. The Protein Data Bank and the challenge of structural genomics
27. Basic local alignment search tool
28. Threading a database of protein cores
29. Measures of threading specificity and accuracy
30. Parser for protein folding units
31. Critical assessment of methods of protein structure prediction (CASP): Round III
32. A measure of success in fold recognition
33. A comparison of sequence and structure protein domain families as a basis for structural genomics
34. The relation between the divergence of sequence and structure in proteins
35. Comparison of conformational characteristics in structurally similar protein pairs
36. Comparison of solvent-inaccessible cores of homologous proteins: Definitions useful for protein modelling
37. Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility
38. Evolution of protein sequences and structures
39. A comprehensive comparison of multiple sequence alignment programs
40. Large-scale comparison of protein sequence alignment algorithms with structure alignments
41. T-Coffee: A novel method for fast and accurate multiple sequence alignment
42. Position-based sequence weights
43. A comparison of position-specific score matrices based on sequence and structure alignments
44. Combination of threading potentials and sequence profiles improves fold recognition
45. Structure classification-based assessment of CASP3 predictions for the fold recognition targets
46. CLUSTAL W: Improving the sensitivity of progressive multiple sequence a alignment through sequence weighting, position-specific gap penalties and weight matrix choice
47. Enhanced genome annotation using structural profiles in the program 3D-PSSM