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This repository contains full data from MHCPEP database, and selected data including independent data sets of proteins and protein fragments, non-binding peptides, lists of T-cell epitopes, and recommendations for scaling and comparison of performance of prediction systems. It can be used in conjunction with IEDB data sets for the development of advanced machine learning and pattern recognition solutions.

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• SciCrunch
• 17 years ago - by Anonymous

The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes. The version 4.0 of database provides information about peptides interacting with TAP and MHC linked autoimmune diseases.

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• SciCrunch
• 17 years ago - by Anonymous

The MHC-Peptide Interaction Database version T (MPID-T) is a new generation database for sequence-structure-function information on T cell receptor/peptide/MHC interactions. It contains all structures of TcR/pMHC and pMHC complexes, with emphasis on the structural characterization of these complexes. MPID-T will facilitate the development of algorithms to predict whether a peptide sequence will bind to a specific MHC allele. The database has been populated with the data from the Protein Data Bank(PDB). The data from the PDB is manually verified and classified, after which each structure is analysed for atomic interactions relevant to MHC-Peptide complex.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.Database for annotated mouse proteins and their occurrence in protein networks. It contains cDNA and protein sequences, annotation, gene models and mapping, FunCat, UCSC Genome Viewer, SIMAP, pseudogenes (Genome Viewer Track), InterPro, and splice variants. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system. To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database. The gene models are based on the RefSeq mouse cDNAs. The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database and the Comprehensive Resource of Mammalian Protein Complexes are linked to the MfunGD dataset. Links to external resources are also provided. MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture.

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• SciCrunch
• 17 years ago - by Anonymous

A database of information on nuclear receptors. Included in the database are sequence information, structural information, and mutation data. Users can BLAST sequences, view 2D structural data, see the chromosomal location of nuclear receptors genes, and utilize other tools found on the website.

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• SciCrunch
• 17 years ago - by Anonymous

metaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes. Phylogenomic information is provided by 2,257 large phylogenetic trees which can be interactively explored. High-throughput tree analysis can also be carried out to identify trees of interest, e.g. trees containing horizontal gene transfers. metaTIGER also provides novel facilities for viewing and comparing the metabolic profiles.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. Database and Browser containing quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?, and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms). This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins.

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• SciCrunch
• 17 years ago - by Anonymous

A free web-oriented database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats. MMsINC is provided by the Molecular Modeling Section in the Department of Pharmaceutical Sciences at the University of Padova, (Italy) in collaboration with the Software Support Services & Development Laboratory (S3D) at the Center for Advanced Studies, Research and Development (CRS4) in Sardinia.

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• SciCrunch
• 17 years ago - by Anonymous

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes.

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• SciCrunch
• 17 years ago - by Anonymous

An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database of metal ion binding sites in RNA. It provides information that allows the classification of and search for specific metal binding motifs (e.g., tandem G-U pairs, loop E motif, A-platform motif). The RNA binding sites of 23 different metal ions are described, the most common of these being Mg2+, Na+, Ca2+, Cd2+ and K+. The user can browse the database or search by PDB or NDB identifier, metal ion, binding motif, type of binding, distance cutoff criteria, experimental conditions (NMR, X-ray, etc.), resolution and R-values, and any combination of the aforementioned criteria or author(s) name. The design and development of the database of metal ion binding sites in RNA is part of a research program which focuses on classification and understanding of RNA motif structure, function, tertiary interactions and their relationships. Using the information contained in our database, we will explore approaches to predicting metal ion binding sites in RNA sequence and structure and to identifying new RNA metal ion binding motifs, which will eventually lead to the design of RNA structures with specific metal binding characteristics.

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• SciCrunch
• 17 years ago - by Anonymous

A database of structural motifs for protein structures related at the family and-or superfamily level. Such motifs among structurally aligned proteins are recognized by the conservation of amino acid preference and solvent inaccessibility and are examined for the conservation of other important structural features like secondary structural content, hydrogen bonding pattern and residue packing. These motifs may form the common core by maintaining a particular spatial orientation pattern when compared across different proteins belonging to the same family or superfamily. Such motifs can also be employed to design and rationalize protein engineering and folding experiments. Therefore, the MegaMotifbase can be a useful resource to gain knowledge about structure and functional relationship of proteins. Alignments are available for download.

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• SciCrunch
• 17 years ago - by Anonymous

A catalog of known and/or predicted biochemical pathways from barrelclover (Medicago trunculata). It features more than 240 pathways with related genes, enzymes, and metabolites. MedicCyc was assembled based on over 225,000 Medicago truncatula ESTs and available genomic sequences. This is a mirror database kindly provided by the MedicCyc group from the SR Nobel Foundation. The initial compilation was manually annotated to remove non plant pathways, and several Medicago-specific pathways including isoflavonoid, lignin, and saponin biosyntheses were modified or added based on available literature. Predicted pathways and annotations in MedicCyc were then verified through comparison with AraCyc and RiceCyc database. MedicCyc can be used as a reference for the study of primary and secondary metabolism of Medicago truncatula as well as for other legume species.

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• SciCrunch
• 17 years ago - by Anonymous

A database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB contains experimentally determined biopolymer structures obtained from the Protein Data Bank. MMDB contains a subset of three-dimensional structures obtained from the Protein Data Bank (PDB), excluding theoretical models. MMDB is a database of ASN.1-formatted records. It was designed for flexibility, and as such, is capable of archiving conventional structural data as well as future descriptions of biomolecules, such as those generated by electron microscopy (surface models).

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• SciCrunch
• 17 years ago - by Anonymous

The Mutation Database for Parkinson's Disease (MDPD) is designed to fulfill the need for information integration so that users can easily retrieve, inspect and enhance their knowledge on PD. The database contains 2391 entries on 202 genes extracted from 576 publications and manually examined by biomedical researchers. Each genetic substitution and the resulting impact are clearly labeled and linked to its primary reference. Every reported gene has a summary page that provides information on the variation impact, mutation type, the studied population, mutation position and reference collection. In addition, MDPD provides a unique functionality for users to compare the differences on the type of mutations among ethnic groups. As such, we hope that MDPD will serve as a valuable tool to bridge the gap between genetic analysis and clinical practice.

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• SciCrunch
• 16 years ago - by Anonymous

Database containing several body fluid proteomes, including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools.

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• SciCrunch
• 17 years ago - by Anonymous

NTDB is a database is a collection of thermodynamic and structural data, experimental methods, conditions and relevant literature citations on nucleic acids. This database is updated continuously. The thermodynamic data of interest can be searched by structural features, thermodynamic parameters, experimental methods and the use of citation. Tools relating to the thermodynamic properties of nucleic acids are also made available in this database and can be applied to predict thermal denaturation profiles, free energy, etc. Some related links are also available. Users are encouraged to deposit new thermodynamic data on nucleic acids to this database.

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• SciCrunch
• 17 years ago - by Anonymous

Database providing a collection of all the existing polymorphic sequences in the Mammalia group. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the mammalian publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank, and the cross-references to the PopSet database. The database content is daily updated, and records are assigned unique and permanent MamPol identification numbers to facilitate cross-database referencing.

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• SciCrunch
• 17 years ago - by Anonymous

Database of gene expression in whole-mount mouse embryos derived from in situ hybridization on mid-gestation mouse embryos. A genome wide screening for genes showing a tissue restricted expression pattern in mid-gestation embryos is performed to identify genes that are likely to play an important role in the regulatory networks controlling pattern formation and organogenesis. The screening provides the basis for imaging the molecular anatomy of the mouse embryo, and for creating a gene resource for a directed functional analysis of developmental processes. The experimental protocol is available. Pattern genes in MAMEP: 1912 Images in MAMEP: 23994

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• SciCrunch
• 17 years ago - by Anonymous

M3D is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains Affymetrix expression compendia for Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis. M3D (Many Microbe Microarrays) was developed by the Gardner Lab at Boston University to facilitate the exchange and analysis of high quality, curated, microbial gene expression data. Currently, the database only includes data obtained using Affymetrix GeneChip technology, because the high quality of the platform facilitates cross-laboratory integration of data sets. The database allows downloading of raw data (CEL files) or preprocessed data that has been uniformly normalized with RMA. M3D also enables convenient web-based expression data exploration and visualization - accessable via the Analysis page.

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• SciCrunch
• 17 years ago - by Anonymous