The Molecular Modeling Database (MMDB) contains 3D macromolecular structures, including proteins and polynucleotides. MMDB contains over 28,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors. [Information of the supplier]
MPtopo is a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. The database is maintained in SQL form using the MySQL server. It can be searched using MPtopoQuerier, a java applet developed for this purpose. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool. MPtopo currently contains a total of 167 proteins with 1028 TM segments. ... [Information of the supplier, modified]
The Nuclear Protein Database (NPD) is a searchable database of information on proteins that are localised to the nucleus of vertebrate cells. The NPD contains information on >1000 vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms. Where appropriate, links to other databases are provided. ... [Information of the supplier]
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. For each family in Pfam you can: Look at multiple alignments, View protein domain architectures, Examine species distribution, Follow links to other databases, View known protein structures. ... [Information of the supplier]
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. ... [Information of the supplier]
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. The RCSB is a member of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniform data. [Information of the supplier]
PubChem contains the chemical structures of small organic molecules and information on their biological activities. PubChem is intended to support the Molecular Libraries and Imaging component of the NIH Roadmap Initiative. PubChem's chemical structure database may be searched on the basis of descriptive terms, chemical properties, and structural similarity. When possible, PubChem's chemical structure records are linked to other NCBI databases. These include the PubMed scientific literature database, for example, and NCBI's protein 3D structure database. PubChem also contains the results of high-throughput biological screening experiments. ... [Information of the supplier]
RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories. We strongly encourage researchers to submit their validated primer and probe sequence, so that other users can benefit from their expertise. The database can be queried using the official gene name or symbol, Entrez or Ensembl Gene identifier, SNP identifier, or oligonucleotide sequence. Different options make it possible to restrict a query to a particular application (Gene Expression Quantification/Detection, DNA Copy Number Quantification/Detection, SNP Detection, Mutation Analysis, Fusion Gene Quantification/Detection), organism (Human, Mouse, Rat, and 17 others) or detection chemistry. Data submission is allowed after free registration whereby you obtain a login name and password. Currently, 3607 real-time PCR assays for 2214 genes are available, submitted by 848 people. ... [Information of the supplier]
The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952)." / "A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. ... [Information of the supplier]
Although several sites of metabolic processes are available to the web browser, they are generally loaded with superfluous information, much of which may not be relevant for malaria parasites. The purpose of this site was to extract the pertinent information from the universal sites and to present them in an educative and informative format. ... [Information of the supplier]