Curator Dashboard

Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.,

• Resource
• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented April 14, 2017. The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL's, etc. that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

This database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A new source of RESP or ESP atomic charge values for small structures or model systems. Its goals are multiple. R.E.DD.B. freely stores and distributes derived RESP or ESP charges of high quality and high reproduciblility within force field library(ies) in the scientific community. However, R.E.DD.B. can also be seen as a tool devoted to reproduce, compare, criticize and improve the different RESP and ESP models. As indicated by its name, R.E.DD.B. deals _only_ with RESP or ESP charges, and not with other types of atomic charges (Mulliken, Gasteiger or Bader analysis...). As previously said, many different procedures are used to derive such RESP or ESP charges, and the charge values are affected by many parameters (Quantum Mechanics programs, algorithms, molecular orientation, molecular conformation, human errors, etc..). Thus, R.E.DD.B. not only stores RESP or ESP charge values, but also the structures and information about the procedure used to derive the reported charge values. Two types of "projects" can be found in R.E.DD.B. - A WHOLE MOLECULE "project", which corresponds to an intact (un-broken) molecule. Examples are small organic or inorganic molecules such as solvent (DMSO, ethanol, cyclohexane etc...), and ligands of proteins or nucleic acids. - A MOLECULE FRAGMENT "project", which corresponds to a part (or fragment) of an organic or inorganic macro-molecule. This means that some atoms have to be removed from the structure(s) used in the charge derivation process to lead to the target fragment(s). Examples are amino-acid (AA) fragments 'NH-CH(R)-CO' where the atomic charges are generally derived using capped amino acids 'ACE-AA-NME', nucleotide fragments originating from the fusion between dimethylphosphate and the corresponding nucleosides, or monosaccharide fragments. These fragments are generally compatible with previously existing ones (available in force field topology databases), and used to construct macro-molecules such as proteins, nucleic acids or polysaccharides.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A database of comprehensive information about mutant phenotypes, reporter-gene expression patterns, flanking sequences of T-DNA insertional sites, seed availability, and others are collected in the database. RMD can be searched by keywords, nucleotide sequence or protein sequence. This database provides three classes of functions: (1) identifying novel genes, (2) identifying regulatory elements, and (3) identifying pattern lines for ectopic expression (misexpression) of target gene at specific tissue or at specific growth stage.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

The Saccharomyces Cerevisiae Morphological Database(SCMD) is a collection of micrographs of budding yeast mutants. Micorgraphs of mutants with altered cell morphology from a set of the haploid MATa deleted strains obtained from EUROSCARF. From the micrographs, disruptant cells are automatically extracted by our novel cell-image processing software.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It provides information about primers and probes that can be used to quantitate human and mouse mRNA by reverse transcription polymerase chain reaction (RTx96PCR) assays. Users can search the QPPD to find: * Primer sets and probes for a given gene * Primer location * Amplicon size * Assay type * Positions of single nucleotide polymorphisms (SNPs) * Literature references * Available I.M.A.G.E. cDNA clones * The Primer Viewer, a graphical representation of the gene and primer sets, which includes hyperlinks to Gene Info from the Cancer Gene Anatomy Project (CGAP) and the CGAP SNP viewer.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Study to surveyed structures of protein-protein interfaces in PDB to carry out structural comparisons of interfaces. Structural comparisons of protein-protein interfaces.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

It provides information on natural and artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, and each entry in the database corresponds to one article which may describe one, several or a number of protein mutants. Each database entry is identified by a serial number and is defined as either natural or artificial, depending on the type of the mutation. For each entry the following are recorded : JOURNAL, TITLE, CROSS-REFERENCE, PROTEIN, N-TERMINAL, CHANGE, FUNCTION, STRUCTURE, STABILITY, etc. CROSS-REFERENCE indicates the code names of the protein given in other databases such as Protein Identification Resources (2). N-TERMINAL shows the N-terminal sequence of five amino acids which may help to show the unambiguous numbering of th e sequence. CHANGE indicates the position and kind of mutations, such as amino acid substitution, insertion and deletion, denoted with a specific notation. Any functional or structural features (FUNCTION, STRUCTURE, STABILITY,etc) observed in the mutant are described immediately after ''CHANGE''. Relative differences in activity and/or stability, in comparison with the wild-type protein, are indicated with symbols (- -),(-),(=),(+) or (+ +). Complete loss of activity is denoted as (0). Data Submission A data submission system was newly prepared in the PMD. We welcome the authors of articles published in academic journals to submit their own mutant data to the PMD. After checking the contents, we will register the data with a unique accession number.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures). The rest of entries are constructed from PDB files for multi-chain protein complexes by leaving only two interacting chains, (in the database nomenclature designators of those chains are appended to the name of the original PDB file). The homo-complexes in this database are the complexes with two monomers having more than 95 % sequence identity. Each entry consists of the X-ray structure taken from the PDB data bank (in the PDB/ folder), sequence file (in the SEQ/ folder) and the data file (in the INF/ folder) where all relevant information is stored. File names consist of PDB ID and extensions .pdb (X-ray structures), .seq (sequence files or .inf (data files). Current implementation of the database accommodates the following information for each entry, separately for larger (denoted as chain A*) and smaller (chain B) components: * Full sequence; * Number of residues; * Number of residues on the interface; * List of interfacial residues; * Number of helices and strands; * Absolute (in �2) and relative interface areas. The database is searchable with respect to majority of the above parameters. Additional search is possible with respect to the PDB ID and protein names. Downloads are possible for both individual entries (as plain text files) and for the whole content or search (checked) result list (as one gzipped file). Supplementary search and download is available for the subset of the database at 40% sequence identity level (the DPPC40 database).

• Resource
• SciCrunch
• 17 years ago - by Anonymous

This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A sister database to ProSite, is constituted of manually created rules that increase the discriminatory power of PROSITE motifs (generally profiles) by providing additional information about functionally and/or structurally critical amino acids and can automatically generate annotation based on PROSITE motifs in the UniProtKB/Swiss-Prot format. Each ProRule is defined in the UniRule format. In addition to these rules corresponding to a unique PROSITE motif, there are also rules triggered by a specific combination of PROSITE motifs called metamotifs. Metamotifs allow the definition of arrangements of domains separated by spacers of variable size, as well as the anchoring to the N- and/or C-termini and the exclusion of a PROSITE motif. ProRule uses the UniRule format that is common to all types of rules created to annotate UniProtKB/Swiss-Prot, including the HAMAP family rules. Each rule contains information used to provide template based annotation associated with the domain or family detected by the PROSITE motif. ProRule is used to create UniProtKB/Swiss-Prot lines with basic and complex annotation derived from the presence of the domain and of biologically critical amino acids: domain name and boundaries, EC number, function, keywords, associated PROSITE patterns, PTMs, active sites, disulfide bonds, etc.). ProRule contains notably the position of structurally and/or functionally critical amino acid(s), as well as the condition(s) they must fulfil to play their biological role(s). Part of these supplementary data are used by ScanProsite that not only provides the protein sequence matched by a profile, but also information about the relevance of biologically meaningful residues, like active sites, binding sites, post-translational modification sites or disulfide bonds, to help function determination

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of interactions between amino acid residues of enzyme and its ligands. Provides summary of interactions between amino acid residues of enzyme and its various ligands including substrate and transition state analogues, cofactors, inhibitors, and products., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

PPNEMA is abioinformatic database of rRNA genes from plant-parasitic nematodes. It consists of a database of ribosomal cistron sequences from various species grouped according to nematode genera, and a search system allowing data to be extracted according to both text and pattern searching. PPNEMA offers to the scientific community a preprocessed archive of plant parasitic nematode sequences useful for nematologists. It is a tool to retrieve plant nematode multialigned sequences for phylogenetic studies or to recognize a nematode by comparing its rDNA sequence with the PPNEMA available genus specific multialignments.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A Plant Proteome DataBase for Arabidopsis thaliana and maize (Zea mays). The PPDB stores experimental data from in-house proteome and mass spectrometry analysis, curated information about protein function, protein properties and subcellular localization. Importantly, proteins are particularly curated for possible (intra) plastid location and their plastid function. Protein accessions identified in published Arabidopsis (and other Brassicacea) proteomics papers are cross-referenced to rapidly determine previous experimental identification by mass spectrometry. All protein-encoding gene models in the Arabidopsis nuclear and organellar genomes, as assembled by TAIR, as well as all maize EST assemblies (ZmGI) as assembled by DFCI Maize Gene Index project. These are all uploaded in PPDB and are linked to each other via a BLAST alignment. Thus every predicted protein in both species can be searched for experimental and other information (even if not experimentally identified).

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A searchable database of pKa values of amino acid residues within proteins. These values have been measured experimentally using a variety of methods, including NMR and the linearized Poisson-Boltzmann equation. This database of protein ionization constants was sourced from the primary literature and contains in excess of 1400 entries. The database contains pKa values for amino acid side-chains, as well as the N and C termini, over 75% of which focus on Glutamate, Lysine, Histidine and Aspartate. These four residues are all key ionizable residues, and therefore the apparent bias is not driven by our selection, but by the available experimental data. Very little data is currently available for Arginine: its pKa value (~12) essentially precludes measurement by titration as proteins will denature at high basic pH.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A database of information on pox viruses. Goals of this project are to acquire and annotate data on poxviruses, and to develop and utilize new tools to facilitate the study of this group of organisms. This basic research is being undertaken with an eye toward the development of novel antiviral therapies, vaccines against human orthopoxvirus infections, new approaches for the environmental detection of virions, and methods to accomplish more rapid diagnosis of disease.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

An integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations. Unlike other databases of similar nature, apart from integrating several coding SNPs (cSNPs) and protein-related information resources, we predict the implications of the non-synonymous SNPs (nsSNPs) using two well known algorithms (SIFT and PolyPhen). The results are presented in an intuitive visualization that depicts the cSNPs mapped onto protein domains and highlights those nsSNPs that are potentially damaging/deleterious or have been reported as disease allelic variants (based on OMIM). The query interface also supports searching for a list of proteins associated with any gene ontology term, pathway, disease term or gene family. Results can also be downloaded as a spreadsheet. The visualization page also provides links to several other related sources and dynamic links to literature references.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A database of quadruplex motifs. It is composed of two parts (EuQuad and ProQuad). EuQuad gives information on quadruplex motifs present in human, chimpanzee, rat and mouse genes. ProQuad contains quadruplex information of 146 prokaryotes. Apart from gene-specific searches QuadBase has a number of other modules. ‘Orthologs Analysis' queries for conserved motifs across species in a user-defined manner; ‘Pattern Search' can be used to fetch specific motifs of interest and the ‘Pattern Finder' tool can search for motifs in any given sequence

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites.

• Resource
• SciCrunch
• 17 years ago - by Anonymous