Literature DB >> 10592233

Increased coverage of protein families with the blocks database servers.

J G Henikoff1, E A Greene, S Pietrokovski, S Henikoff.   

Abstract

The Blocks Database WWW (http://blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PROSITE and PRINTS. Other new features include improved Block Searcher statistics, searching with NCBI's IMPALA program and 3D display of blocks on PDB structures.

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Year:  2000        PMID： 10592233      PMCID： PMC102407          DOI： 10.1093/nar/28.1.228

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  20 in total

1.  Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.

Authors:  S Henikoff; J G Henikoff; S Pietrokovski
Journal:  Bioinformatics       Date:  1999-06       Impact factor: 6.937

2.  Automated assembly of protein blocks for database searching.

Authors:  S Henikoff; J G Henikoff
Journal:  Nucleic Acids Res       Date:  1991-12-11       Impact factor: 16.971

3.  Automated construction and graphical presentation of protein blocks from unaligned sequences.

Authors:  S Henikoff; J G Henikoff; W J Alford; S Pietrokovski
Journal:  Gene       Date:  1995-10-03       Impact factor: 3.688

4.  Searching databases of conserved sequence regions by aligning protein multiple-alignments.

Authors:  S Pietrokovski
Journal:  Nucleic Acids Res       Date:  1996-10-01       Impact factor: 16.971

5.  Embedding strategies for effective use of information from multiple sequence alignments.

Authors:  S Henikoff; J G Henikoff
Journal:  Protein Sci       Date:  1997-03       Impact factor: 6.725

Review 6.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

7.  Score distributions for simultaneous matching to multiple motifs.

Authors:  T L Bailey; M Gribskov
Journal:  J Comput Biol       Date:  1997       Impact factor: 1.479

8.  RASMOL: biomolecular graphics for all.

Authors:  R A Sayle; E J Milner-White
Journal:  Trends Biochem Sci       Date:  1995-09       Impact factor: 13.807

9.  Protein family classification based on searching a database of blocks.

Authors:  S Henikoff; J G Henikoff
Journal:  Genomics       Date:  1994-01-01       Impact factor: 5.736

10.  Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.

Authors:  R L Tatusov; S F Altschul; E V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  1994-12-06       Impact factor: 11.205
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  91 in total

1.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Authors:  R Apweiler; T K Attwood; A Bairoch; A Bateman; E Birney; M Biswas; P Bucher; L Cerutti; F Corpet; M D Croning; R Durbin; L Falquet; W Fleischmann; J Gouzy; H Hermjakob; N Hulo; I Jonassen; D Kahn; A Kanapin; Y Karavidopoulou; R Lopez; B Marx; N J Mulder; T M Oinn; M Pagni; F Servant; C J Sigrist; E M Zdobnov
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  The MetaFam Server: a comprehensive protein family resource.

Authors:  K A Silverstein; E Shoop; J E Johnson; A Kilian; J L Freeman; T M Kunau; I A Awad; M Mayer; E F Retzel
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  TIGRFAMs: a protein family resource for the functional identification of proteins.

Authors:  D H Haft; B J Loftus; D L Richardson; F Yang; J A Eisen; I T Paulsen; O White
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  The EMOTIF database.

Authors:  J Y Huang; D L Brutlag
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

5.  The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments.

Authors:  J Murvai; K Vlahovicek; E Barta; S Pongor
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

6.  iProClass: an integrated, comprehensive and annotated protein classification database.

Authors:  C H Wu; C Xiao; Z Hou; H Huang; W C Barker
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

7.  PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.

Authors:  J Qian; B Stenger; C A Wilson; J Lin; R Jansen; S A Teichmann; J Park; W G Krebs; H Yu; V Alexandrov; N Echols; M Gerstein
Journal:  Nucleic Acids Res       Date:  2001-04-15       Impact factor: 16.971

8.  Website review: interPro (the integrated resource of protein domains and functional sites).

Authors:  C Southan
Journal:  Yeast       Date:  2000-12       Impact factor: 3.239

9.  Sentra, a database of signal transduction proteins.

Authors:  Natalia Maltsev; E Marland; G X Yu; S Bhatnagar; R Lusk
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

10.  PRINTS and PRINTS-S shed light on protein ancestry.

Authors:  T K Attwood; M J Blythe; D R Flower; A Gaulton; J E Mabey; N Maudling; L McGregor; A L Mitchell; G Moulton; K Paine; P Scordis
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971
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