The following external databases and analysis tools are cross-referenced on the JenaLib pages
| BMRB | BioMagResBank - a repository for data from NMR spectroscopy on proteins, peptides and nucleic acids. |
| CATH | Protein Structure Classification |
| CE | Databases and Tools for 3-D Protein Structure Comparison and Alignment Using the Combinatorial Extension (CE) Method |
| Dali | Automatic fold classification based on structure-structure alignment of proteins |
| DIP | Database of Interacting Proteins (includes currently mainly proteins from yeast, human, mouse, Helicobacter pylori) |
| DSSP | The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). |
| EDS | Electron Density Server . The Uppsala Electron Density Server Project aims to provide the protein crystallographic community with a service for evaluating the quality of structures deposited in the Protein Data Bank. Various tools are provided for indicating goodness of fit between the deposited structures and the experimental data represented by the structure factors. |
| ENSEMBL | Ensembl presents up-to-date sequence data and the best possible automatic annotation for metazoan genomes. Available now are human, mouse, rat,fugu, zebrafish, mosquito, Drosophila, C. elegans, and C. briggsae, Others will be added soon. |
| ENZYME | ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. |
| GeneCensus | GeneCensus Genome Comparisons |
| Gene Ontology | The goal of the Gene Ontology project is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes. GO is one of the controlled vocabularies of the Open Biomedical Ontologies. |
| GRASS | Graphical Representation and Analysis of Structure Server |
| Search Engine and Web Directory | |
| HSSP | The HSSP database is a database of homology-derived secondary structure of proteins. |
| InterPro | The databases SWISS-PROT, TrEMBL, PROSITE, PRINTS, Pfam, SMART and ProDom joined forces to launch an Integrated Resource of Protein Families, Domains and Sites, abbreviated InterPro. |
| LPC/CSU | Ligand-Protein Contacts & Contacts of Structural Units |
| MDB | The Metalloprotein site Database and Browser, is the first step towards developing a distributed enviroment for interactive metalloprotein design. It is designed to provide the basic data and tools for geometrical and functional query of existing metal containing sites. It will allow quantitative analysis of the data and will be based on the current Protein Data Bank release, as well as in-house structures (TSRI). Automated tools for computational recognition of metal sites and its characteristics, will assure that the MDB will be always up-to-date. |
| MMDB | NCBI's structure database is called MMDB (Molecular Modelling DataBase), and it is a subset of three-dimensional structures obtained from the Brookhaven Protein DataBank (PDB), excluding theoretical models. |
| ModBase | Database of Comparative Protein Structure Models |
| MSD | EBI Macromolecular Structure Database - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). |
| NDB | The Nucleic Acid Database (NDB) assembles and distributes structural information about nucleic acids. |
| OCA | A browser database for structure function. (similar to the old PDB). |
| OMIM(tm) Online Mendelian Inheritance in Man | This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information. |
| OPM | Orientation of Proteins in Membranes |
| PDBsum | Summaries and structural analyses of PDB data files |
| Pfam | Protein families database of alignments and hidden Markov models |
| PQS | The Protein Quaternary Structure file server ( PQS ) is an internet resource that makes available coordinates for likely quaternary states for structures contained in the Brookhaven Protein Data Bank (PDB) that were determined by X-ray crystallography. |
| PRESAGE | PRESAGE is a collaborative resource for structural genomics. It provides a database of proteins, each of which has a collection of annotations reflecting current experimental status, structural assignments, models, and suggestions. PRESAGE is a tool for scientists to keep track of structural knowledge of their proteins of interest. |
| PROCHECK | Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. |
| ProDom | ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases. |
| PDB | International repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR. |
| ProtoMap | ProtoMap+ is an automatic hierarchical classification of all SWISSPROT and TrEMBL proteins. |
| PubMed | NLM's (National Library of Medicine) search service to access the 9 million citations in MEDLINE and Pre-MEDLINE (with links to participating on-line journals), and other related databases. |
| RNAbase | RNABase consolidates all RNA containing structures from both the NDB and RCSB (formerly PDB). Every entry is automatically checked for conformational errors. |
| scop | Structural Classification Of Proteins |
| SMART | Simple Modular Architecture Research Tool |
| STING | STING is a WWW tool for the simultaneous display of information about macromolecule structure and sequence. |
| SYSTERS | Classification of sequences from SWISS-PROT and PIR into disjoint family clusters and hierarchically into superfamily and subfamily clusters. |
| SWISS-PROT | SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc), a minimal level of redundancy and high level of integration with other databases. |
| WHAT_CHECK | WHAT_CHECK are the biopolymer structure verification tools of the program WHAT_IF. |
| XdomView | The objective of the program is to provide graphical visualization of domain regions in protein 3D structures and the intron-exon boundary regions in homologous protein sequences. |
Last update: 09-02-2006
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