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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

LumbriBASE is aa research tool for both Earthworm biology and environmental pollution monitoring.It provides a simple, easy-to-use access point to the publicly available Lumbricus rubellus sequence and functional data. It is a research tool for both Earthworm biology and environmental pollution monitoring. It is currently being developed by the Worm Consortium.

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• SciCrunch
• 17 years ago - by Anonymous

LPFC is a database of structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

The lipoxygenases database (LOX-DB) aims to be a web accessible compendium of information in particular on the mammalian members of this multigene family. This resource includes molecular structures, reference data, tools for structural and computational analysis as well as links to related information maintained by others. The data can be retrieved by the use of various search options and analyzed applying publicly available visualization tools. Lipoxygenases are a family of enzymes involved in a variety of human diseases like inflammation, asthma, artherosclerosis and cancer.

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• SciCrunch
• 17 years ago - by Anonymous

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications.

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• SciCrunch
• 17 years ago - by Anonymous

Database that integrates information on sequence and structure of lipases and related proteins sharing the same a/b hydrolase fold to facilitate protein engineering. Users can browse the database by classification, organism, hierarchic tree, and structure. They can also perform homology searches against the lipase database, and query the Lipase Engineering Database using SQL.

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• SciCrunch
• 14 years ago - by Anonymous

LIS is a publicly accessible legume resource that integrates genetic and molecular data from multiple legume species and enables cross-species genomic, transcript and map comparisons. The intent of the LIS is to help researchers leverage data-rich model plants to fill knowledge gaps across crop plant species and provide the ability to traverse between interrelated data types. LIS, a component of the Model Plant Initiative (MPI), is being developed as part of a cooperative research agreement between the National Center for Genome Resources (NCGR) and the USDA Agricultural Research Service (ARS).

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• SciCrunch
• 17 years ago - by Anonymous

Knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.Provides information on gene functions (as annotated or supposed by literature from homologous organisms) , protein expression levels under defined experimental conditions ,subcellular localization of proteins (expected and/or experimentally validated) , biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology.

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• SciCrunch
• 17 years ago - by Anonymous