Literature DB >> 11125090

The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

J S Garavelli1, Z Hou, N Pattabiraman, R M Stephens.   

Abstract

The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute-Frederick Advanced Biomedical Computing Center at these web sites: http://www. ncifcrf.gov/RESID, http://www.ncifcrf.gov/NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid .html, http://pir.georgetown.edu/pirwww/dbinfo/nrl3d .html

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Year:  2001        PMID: 11125090      PMCID: PMC29832          DOI: 10.1093/nar/29.1.199

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


  7 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Protein Information Resource: a community resource for expert annotation of protein data.

Authors:  W C Barker; J S Garavelli; Z Hou; H Huang; R S Ledley; P B McGarvey; H W Mewes; B C Orcutt; F Pfeiffer; A Tsugita; C R Vinayaka; C Xiao; L S Yeh; C Wu
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

Review 3.  From primary structure to function: biological insights from large-molecule mass spectra.

Authors:  N L Kelleher
Journal:  Chem Biol       Date:  2000-02

4.  NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment.

Authors:  N Pattabiraman; K Namboodiri; A Lowrey; B P Gaber
Journal:  Protein Seq Data Anal       Date:  1990-10

5.  A relational database for sequence-specific protein NMR data.

Authors:  B R Seavey; E A Farr; W M Westler; J L Markley
Journal:  J Biomol NMR       Date:  1991-09       Impact factor: 2.835

6.  RASMOL: biomolecular graphics for all.

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

7.  Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database.

Authors:  J R Yates; J K Eng; A L McCormack; D Schieltz
Journal:  Anal Chem       Date:  1995-04-15       Impact factor: 6.986

  7 in total
  7 in total

1.  Protein Information Resource: a community resource for expert annotation of protein data.

Authors:  W C Barker; J S Garavelli; Z Hou; H Huang; R S Ledley; P B McGarvey; H W Mewes; B C Orcutt; F Pfeiffer; A Tsugita; C R Vinayaka; C Xiao; L S Yeh; C Wu
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  The Protein Information Resource: an integrated public resource of functional annotation of proteins.

Authors:  Cathy H Wu; Hongzhan Huang; Leslie Arminski; Jorge Castro-Alvear; Yongxing Chen; Zhang-Zhi Hu; Robert S Ledley; Kali C Lewis; Hans-Werner Mewes; Bruce C Orcutt; Baris E Suzek; Akira Tsugita; C R Vinayaka; Lai-Su L Yeh; Jian Zhang; Winona C Barker
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 3.  Bioinformatics methods to predict protein structure and function. A practical approach.

Authors:  Yvonne J K Edwards; Amanda Cottage
Journal:  Mol Biotechnol       Date:  2003-02       Impact factor: 2.695

4.  ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry.

Authors:  Richard D LeDuc; Gregory K Taylor; Yong-Bin Kim; Thomas E Januszyk; Lee H Bynum; Joseph V Sola; John S Garavelli; Neil L Kelleher
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

5.  SAND, a new protein family: from nucleic acid to protein structure and function prediction.

Authors:  A Cottage; Y J Edwards; G Elgar
Journal:  Comp Funct Genomics       Date:  2001

6.  Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access.

Authors:  Fernanda L Sirota; Sebastian Maurer-Stroh; Birgit Eisenhaber; Frank Eisenhaber
Journal:  Proteomics       Date:  2015-07       Impact factor: 3.984

7.  ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry.

Authors:  Leonid Zamdborg; Richard D LeDuc; Kevin J Glowacz; Yong-Bin Kim; Vinayak Viswanathan; Ian T Spaulding; Bryan P Early; Eric J Bluhm; Shannee Babai; Neil L Kelleher
Journal:  Nucleic Acids Res       Date:  2007-06-22       Impact factor: 16.971

  7 in total

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