Protein domain identification and improved sequence similarity searching using PSI-BLAST

Proteins: Structure, Function and Genetics

Volumn 48, Issue 4, 2002, Pages 672-681

  George, Richard A ^a   Heringa, Jaap ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

Domains; Genome; Modules; PSI BLAST; Sequence

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; COMPUTER PROGRAM; INTERMETHOD COMPARISON; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; TECHNIQUE;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPETITIVE SEQUENCES, AMINO ACID; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0036721254     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10175     Document Type: Article

References (46)

1. Shuffled domains in extracellular proteins
2. The multiplicity of domains in proteins
3. Three-dimensional domain duplication, swapping and stealing
4. Tertiary structure of an immunoglobulin-like domain from the giant muscle protein titin: A new member of the I set
5. The KH module has an alpha beta fold
6. Protein fold irregularities that hinder sequence analysis
7. Identification of cell-binding sites on the Laminin alpha 5 N-terminal domain by site-directed mutagenesis
8. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
9. A combined algorithm for genome-wide prediction of protein function
10. The prediction of protein domains
11. Prediction of the location of structural domains in globular proteins
12. A possible way for prediction of domain boundaries in globular proteins from amino acid sequence
13. Domain size distributions can predict domain boundaries
14. SnapDRAGON - A method to delineate protein structural domains from sequence data
15. The Pfam protein families database
16. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
17. SMART: Identification and annotation of domains from signalling and extracellular protein sequences
18. DOMO: A new database of aligned protein domains
19. Identification of common molecular subsequences
20. Improved tools for biological sequence comparison
21. Basic local alignment search tool
22. Improved sensitivity of profile searches through the use of sequence weights and gab excision
23. Dynamic sequence databank searching with templates and multiple alignment
24. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
25. Profile analysis: Detection of distantly related proteins
26. Improving the sensitivity of the sequence profile method
27. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
28. A workbench for large-scale sequence homology analysis
29. Ballast: Blast post-processing based on locally conserved segments
30. Automated search of natively folded fragments for high-throughput structure determination in structural genomics
31. Whole genome protein domain analysis using a new method for domain clustering
32. Non-globular domains in protein sequences: Automated segmentation using complexity measures
33. Domain assignment for protein structures using a consensus approach: Characterization and analysis
34. Circular permutations of natural protein sequences: Structural evidence
35. OBSTRUCT: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity
36. Two strategies for sequence comparison: Profile-preprocessed and secondary structure-induced multiple alignment
37. Local weighting schemes for protein multiple sequence alignment
38. Identification of homologous core structures
39. Protein structural domain identification
40. Hidden Markov models for detecting remote protein homologies
41. Profile hidden Markov models
42. Searching databases to find protein domain organization
43. Modularity and homology: Modelling of the type II module family from titin
44. A method to recognise distant repeats in protein sequences
45. The REPRO server: Finding protein internal sequence repeats through the Web