E-MSD: an integrated data resource for bioinformatics.

@article{Golovin2004EMSDAI,
  title={E-MSD: an integrated data resource for bioinformatics.},
  author={Adel Golovin and Thomas J. Oldfield and John G. Tate and Sameer Velankar and Geoffrey John Barton and Harry Boutselakis and Dimitris Dimitropoulos and Jo{\"e}l Fillon and A. Hussain and John M. C. Ionides and Melford John and Peter A. Keller and Evgeny B. Krissinel and P. McNeil and Avi Naim and Richard H. Newman and Anne Pajon and J. Pineda and Abdelkrim Rachedi and J. Copeland and Andrey Sitnov and Siamak Sobhany and Antonio Suarez-Uruena and Ganesh Jawahar Swaminathan and Mohammed Tagari and Swen Tromm and Wim F. Vranken and Kim Henrick},
  journal={Nucleic acids research},
  year={2004},
  volume={32 Database issue},
  pages={
          D211-6
        }
}
The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces… 

Figures and Tables from this paper

PDBe: Protein Data Bank in Europe
TLDR
Recently developed, extended or improved services, including an animated structure-presentation widget, a widget to graphically display the coverage of any UniProt sequence in the PDB, chemistry- and taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and analysis results (Vivaldi) are described.
A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules.
TLDR
It is the aim to guide researchers outside the structure biology field in getting the most out of the 3D structure resources and to describe these resources from a user's point of view and from a comparative perspective.
MobiDB: a comprehensive database of intrinsic protein disorder annotations
TLDR
MobiDB features experimental annotations for 17 285 proteins, covering the entire PDB and predictions for the SwissProt database, with 565 200 annotated sequences, and a weighted consensus disorder used to classify disordered regions into flexible and constrained disorder.
Analytical Processing of PDB Ligand Fragments and Protein Environment directly on the Web
The PDB protein-ligand complexes are the main public resource that provides detailed chemical environment information for atomic level interactions between the ligand and the protein. In order to
Structural Bioinformatics: From the Sequence to Structure and Function
TLDR
High-throughput methods for the determination of protein structures provide the information needed to build structure-activity relationships and Voronoi tessellations are used to quantify the macromolecular interfaces.
Integrating Genomic and Proteomic Data: The Integr8 Project
TLDR
The Integr8 project has been developed to provide an integration layer for the exploitation of genomic and proteomic data, and an entity-centric view of complete genomes and proteomes is offered.
Public web-based services from the European Bioinformatics Institute
TLDR
A detailed introduction to the interactive analysis systems that are available from the EBI are provided and a brief introduction to other, related services are provided.
Molecular characterization and evolutionary plasticity of protein-protein interfaces
TLDR
Molecular characterization of hot-spots performed using PICCOLO probes the molecular basis underlying this important phenomenon leading to the possibility of predictive methods to identify hot- Spots in silico, as well as procedures to derive environment-specific substitution tables.
CCP 4 SOFTWARE SUITE : HISTORY , EVOLUTION , CONTENT , CHALLENGES AND FUTURE DEVELOPMENTS
Collaborative Computational Project Number 4 (CCP4) in Protein Crystallography is a public resource for producing and supporting a world-leading, integrated Suite of programs that allows researchers
A structural keystone for drug design
TLDR
A web resource bridging protein and ligand databases that integrates many well-known databases such as Swiss-Prot, SCOP, ENZYME and others and can be used to identify promising drug candidates.
...
...

References

SHOWING 1-10 OF 16 REFERENCES
The InterPro Database, 2003 brings increased coverage and new features
TLDR
The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications, an increase of nearly 15% since the inception of Inter pro.
Announcing the worldwide Protein Data Bank
TLDR
The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform, and provides a mechanism to ensure consistent data for software developers and users worldwide.
SCOP database in 2004: refinements integrate structure and sequence family data
TLDR
A refinement of the SCOP classification is initiated, which introduces a number of changes mostly at the levels below superfamily, and modernization of the interface capabilities of SCOP allowing more dynamic links with other databases is started.
Assigning genomic sequences to CATH
TLDR
The CATH Dictionary of Homologous Superfamilies (DHS), which contains validated multiple structural alignments annotated with consensus functional information for evolutionary protein superfamilies, has been updated to include annotations associated with sequence relatives identified in GenBank.
The EMBL Nucleotide Sequence Database
TLDR
The EMBL Nucleotide Sequence Database incorporates, organizes and distributes nucleotide sequences from public sources, and the EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases as well as many other specialist molecular biology databases.
IntAct: an open source molecular interaction database
TLDR
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins.
UniProt: the Universal Protein knowledgebase
TLDR
The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.
The KEGG resource for deciphering the genome
TLDR
A knowledge-based approach for network prediction is developed, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes.
The Pfam protein families database
TLDR
The latest version (4.3) of Pfam contains 1815 families, which match 63% of proteins in SWISS-PROT 37 and TrEMBL 9.
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
TLDR
The Gene Ontology Annotation database aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of theGene Ontology (GO).
...
...