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EBI / EMBL-EBI - The European Bioinformatics Institute
Supplies an access to several biological data resources and bioinformatics services. EBI is a platform that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems, pathways, ontologies and literature. Databases, tools, as well as web services are provided for sharing data, performing queries and analyzing results. Users can also deposit their data through a data submission page. All the resources are freely available without restriction, with few exceptions.
ModBase
A queryable database of annotated protein structure models. ModBase models are derived by ModPipe, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database also includes the fold assignments and alignments on which the models were based. ModBase contains theoretically calculated models, which may contain significant errors, not experimentally determined structures. Thus, special care is taken to assess the quality of the models. In addition to the protein structure models, ModBase contains information about putative ligand binding sites, SNP annotation, and protein-protein interactions.
PDBsum
Provides overviews and pictorial analyses of the experimentally determined models of macromolecular structures in the Protein Data Bank (PDB). PDBsum provides schematic diagrams to visualize different aspects of the protein molecule(s) in the structure, together with the molecules they interact with. Links to references and citations of the key reference are also provided. The database also includes a full PROCHECK assessment of each protein’s geometry, highlighting regions that are in some way unusual. Users can upload their own structures for analysis.
PDB_REDO
Optimizes crystallographic structure models. PDB_REDO contains algorithm which allows the setting up of an automated decision making system. This system serves for refinement, rebuilding and validation. The PDB_REDO databank includes protein data bank (PDB) entries with electron density maps, a list of model changes and model validation data. It helps about structural biology project. The protocol of the databank allows to treat the entries to reduce the effects of differences in age, software, and depositors.
PDBj / Protein Data Bank Japan
Maintains a centralized PDB archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. The Protein Data Bank Japan is a database that provides a wide range of services and tools for analyzing structures and functions of proteins. It provides its own data viewer, integrated tools and derived databases in order to facilitate structural biology and bioinformatics research from different perspectives than other members of the wwPDB.
GTOP / Genomes TO Protein Structures and Functions database
Compiles several annotations of 3D structures, protein families, functions about proteins. GTOP intends to supply annotations of all the amino acid sequences of proteins derived from all the completely sequenced genomes. Users can make searches about a specific features or species. In addition, the database provides a summary section which allows to view comparative statistics including the ratio of 3D annotations in each genome, the frequencies of SCOP folds as well as superfamilies, or Pfa PROSITE motifs.
Phospho3D
Supplies a repository composed of 3D structures of phosphorylation sites (P-sites) stemmed from the Phospho.ELM database. Phospho3D enhances data from the previous database at the residue level with annotations and structural information. Moreover, it gathers results of a large-scale structural comparison procedure to allow identification of new putative phosphorylation sites. Additionally, it offers a tool which permit to compare a protein structure to the collected dataset.
DBAli
Gathers comparison of protein structures. DBAli is a database that contains pairwise and multiple structure alignments of protein structures in the Protein Data Bank (PDB). It also includes five tools that use the structural relationships in the repository. These tools can be employed to annotate the functions of protein structures whose functions are not yet known. The database also provides links to the MODBASE, LigBase, PIBASE, PDB, CATH, SCOP, PFamA, InterPro, Enzyme and GO databases.
FLAGdb++
Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge.
SoyKB / Soybean Knowledge Base
A comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja.
SFLD / The Structure–Function Linkage Database
A manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. SFLD focuses on the identification of specific sequence and structure attributes reflected in protein similarity that typify specific reactions or substrate specificities. It links enzyme sequence, structure and molecular function into a hierarchical classification scheme, grouped by enzyme superfamilies. Each superfamily in the SFLD is subdivided into successive levels of increasing specificity in sequence similarity and associated functional properties.
PSI SGKB / Protein Structure Initiative Structural Genomics Knowledgebase
Provides results of the protein structure initiative (PSI). PSI SGKB is a knowledge base that supplies access to the annotated protein structures, associated functional predictions, experimental protocols and tracking information and more. This resource integrates structural information with relevant scientific information from external data resources. Moreover, it informs user about a vast array of technologies, protein production protocols and software applications.
ProtCid / Protein Common interfaces database
A database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). Such interfaces, especially of homologous but non-identical proteins, have been associated with biologically relevant interactions. In ProtCID, protein chains in the protein data bank (PDB) are grouped based on their PFAM domain architectures. For a single PFAM architecture, all the dimers present in each CF are constructed and compared with those in other CFs that contain the same domain architecture. Interfaces occurring in two or more CFs comprise an interface cluster in the database.
MegaMotifbase
Gathers structural segments or motifs for protein structures. MegaMotifbase provides a compilation of structural motifs identified through a completely automated method for large number of families and superfamilies of proteins. Motifs contained in the database can assist in the identification of new potential members of an existing family and/or superfamily. MegaMotifbase provides the application of sequence–structural templates in three different areas: multimotif-based sequence search, multiple sequence alignment and homology modeling.
FSN / Flexible Structural Neighborhood
Compiles structural neighbors of proteins deposited in the Protein Data Bank (PDB). FSN allows to search by a PDB code as a query and provides a list of structurally similar proteins sorted by increasing P-values, as well as links to various statistics about this group of proteins. The database provides a table lists structurally similar proteins with each individual protein in a single row, providing detailed information about each comparison and links to PDB and detailed FATCAT result page.
ccPDB / Compilation and Creation of datasets from PDB
Hosts data sets compiled from the literature and Protein Data Bank (PDB). ccPDB collects and compiles data sets from the literature used for developing bioinformatics methods to annotate the structure and function of proteins. The data sets were derived from the latest release of PDB using standard protocols. Furthermore, ccPDB implements a powerful module for creating a wide range of customized data sets from the current release of PDB. This is a flexible module that allows users to create data sets using a simple six step procedure. In addition, a number of web services have been integrated in ccPDB, which include submission of jobs on PDB-based servers, annotation of protein structures and generation of patterns. This database maintains more than 30 types of data sets such as secondary structure, tight-turns, nucleotide interacting residues, metals interacting residues, DNA/RNA binding residues and so on.
Heme Protein Database
Provides information heme protein structure–function relationships. Heme Protein Database is a web-based resource for wild-type heme protein structure–function analysis. The database couples the structural information of a unique set of non-redundant heme proteins from the PDB with their electrochemical function collected from the primary literature. It allows global analysis of the structural factors that influence the midpoint reduction potential of wild-type heme proteins near physiological pH.
AH-DB / Apo and Holo structures DataBase
Provides sophisticated interfaces for searching apo–holo structure pairs. AH-DB allows users to explore conformational transitions from apo structures to the corresponding holo structures. It contains about 746 300 apo–holo structure pairs of 3600 proteins from about 700 organisms. This database offers functions to categorize molecules into proteins, nucleic acids, ligands and ions and identifies map molecules in different Protein Data Bank (PDB) entries.
AmyPro
Offers a sequence screening service allowing users to screen sequences of interest for matching fragments with validated amyloidogenic regions. AmyPro provides comprehensive information on the entry sequences, including (i) precursor proteins, (ii) experimentally validated amyloidogenic sequence regions, (iii) short description of the functional relevance of their soluble and amyloid states, and (iv) list of the experimental techniques used to discover and investigate the amyloid state.
SURFACE / SUrface Residues and Functions Annotated Compared and Evaluated
Stores and spreads the results of a large-scale local surface comparison experiment. SURFACE is a relational database that allows scientific community to retrieve non-obvious functional similarities detected between proteins of known 3D structure. This online resource can be a useful resource for scientific research, providing information about protein functions inferred from different sources and allowing a structural alignment to be obtained easily.
ValidatorDB
Offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries.
ChannelsDB
Provides information about the channels (pores and tunnels) found in entries from the Protein Data Bank (PDB). ChannelsDB is a resource that contains information about the presence and positions of channels in biomacromolecular structures and about local geometrical properties and residues lining the channel and their physicochemical properties. It can be useful for analysis which includes the transport of ligands and other small molecules within biomacromolecular structures.
HSPIR / Heat Shock Protein Information Resource
Delivers information on six major heat shock protein (HSP) families across various genomes. HSPIR is stored following detailed sub-classification based on HSPs’ domain, structural organization and localization. It contains about 10 000 entries, from six manually-curated kingdoms, that expose all the major model organisms and about 300 3D structures. This tool can be useful for comparative analysis and explore additional physiological functions of HSPs in different species.
Cyclo-lib
A database with structural and dynamic analysis obtained from computational MD simulation trajectories of native and modified cyclodextrins (CDs) in explicit water molecules. Cyclo-lib currently includes 70 cyclodextrins typically employed for fundamental and industrial research. Tools for comparative analysis between different cyclodextrins, as well as to restrict the analysis to specific time-segments within the trajectories are also available. Cyclo-lib provides not only the most probable structures and a detailed analysis of a large number of CDs in aqueous solution but also the parameter files required to perform more complex simulation studies including docking, aggregation or adsorption to interfaces.
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