Tag: structure

Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the re ...

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synth ...

Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'small’ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, et ...

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More in ...

The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.

The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and p ...

Established in 1965, the Cambridge Structural Database (CSD) is the a repository for small-molecule organic and metal-organic crystal 3D structures. Database records are automatically checked and manually curated by one of our expert in-house scienti ...

The Protein Quaternary Structure file server (PDBePISA) is an internet resource that makes available coordinates for likely quaternary states for structures contained in the Brookhaven Protein Data Bank (PDB) that were determined by X-ray crystallogr ...

The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated ...

The SCOP database is a curated both manually and with the use of automated tools. This freely available resource aims to provide a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is know ...

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps ...

VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrat ...

PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in ...

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. It is a founding member of the worldwide Protein Data Bank which collects, organises a ...

The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organis ...

This freely accessible database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for clas ...

PhosphoSite Plus provides extensive information on mammalian post-translational modifications (PTMs). The resource supersedes PhosphoSite a mammalian protein database that provides information about in vivo phosphorylation sites.

The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center ...

The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions ...

BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scie ...

NeuroMorpho.Org is a centrally curated inventory of 3D digitally reconstructed neurons associated with peer-reviewed publications. The goal of NeuroMorpho.Org is to provide dense coverage of available reconstruction data for the neuroscience communit ...

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIP ...

PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.

The Nucleic Acids Database contains information about experimentally-determined nucleic acids and complex assemblies. NDB can be used to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and ...

VIPERdb is a database for icosahedral virus capsid structures. The emphasis is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.

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, genome, and sequen ...

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and chemical tools for human pathogens. The TDR Target Project was started in 2005 after a call for applic ...

This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs ...

DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.

MobiDB is a database of intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations. The database ...

The Crystallography Open Database (COD) is a project that aims to gather all available inorganic, metal-organic and small organic molecule structural data in one database.

The Open Provenance Model (OPM) is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. ( ...

CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical c ...

Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. Sequence data from UniProtKB and Ensembl for domains with no experimentally determined structures are s ...

The Protein Circular Dichroism Data Bank (PCDDB) is an open-access online repository for protein circular dichroism spectral- and meta-data. Users may freely extract and deposit validated data and the validation process is conveniently integrated int ...

The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.

IMGT/3Dstructure-DB (1,2) is the three-dimensional (3D) structure database of IMGT®, the international ImMunoGenetics information system® (3,4) that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT ...

The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in ...

The international glycan structure repository for glycans published in the literature. Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered and have an accession number assigned as ...

PASS2 contains alignments of structural motifs of protein superfamilies. PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies). PASS2 con ...

The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces ...

The Structural Biology Data Grid (SBGrid-DG) community-driven repository to preserve primary experimental datasets that support scientific publications. The SBGrid Data Bank is an open source research data management system enabling Structural Biolog ...

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure align ...

Curated repository for small angle scattering data and models. SASBDB contains X-ray (SAXS) and neutron (SANS) scattering data from biological macromolecules in solution.

canSAR is an integrated cancer research and drug discovery resource that brings together large-scale data from different disciplines and allows query and exploration to help cancer research and drug discovery.

ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.

The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques.

ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.

IMGT-ONTOLOGY provides a specific vocabulary of the terminology to be used in immunogenetics and immunoinformatics. The ontology allows for the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional and three-dimensi ...

SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs). SNPeffect primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. Further, SNPeffect holds pe ...

Neuroimaging Informatics Tools and Resources Collaboratory Resources Registry (NITRC-R) describes software tools and resources, vocabularies, test data, and databases. It is intended to extend the impact and longevity of previously funded neuroimagin ...

The Carbohydrate Structure Database (CSDB) contains manually curated natural carbohydrate structures, taxonomy, bibliography, NMR data and more. The Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases were merged in 2015, becoming the CSDB, to impr ...

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.

Predicted structures of internal transcribed spacer 2 (ITS2)

The ASTRAL compendium provides a set of tools and databases designed to aid investigators in the analysis of protein structure, particularly through the use of sequence comparison. Astral augments SCOP, a manual classification of protein domains acco ...

ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand o ...

PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a collaborative effort between PDBe and ...

MetalPDB is a resource aimed at conveying the information available on the three-dimensional structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representat ...

FuzDB compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database ha ...

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

MINAS contains the exact geometric information on the first and second-shell coordinating ligands of every metal ion present in nucleic acid structures that are deposited in the PDB and NDB. Containing also the sequence information of the binding poc ...

Nearest Neighbor parameters for predicting RNA folding

The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature) is a collection of experimentally-verified intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. IDEAL ...

The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is invo ...

caNanoLab is a data sharing portal designed to facilitate information sharing across the international biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support for the ...

Genome3D is a resource that provides structural annotation and 3D models of genomes of model organisms such as human, yeast and E.coli. The database can be used to predict protein structures that have not yet been identified. Genome3D uses structural ...

Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.

WALTZ-DB 2.0 is a database for characterizing short peptides for their amyloid fiber-forming capacities. The majority of the data comes from electron microscopy, FTIR and Thioflavin-T experiments done by the Switch lab. Apart from that class of data ...

RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that contain secondary structure motifs such as mismatches, (a)symmetric interna ...

Validated NMR structures of proteins and nucleic acids.

The Protein Structural Change DataBase (PSCDB) presents the structural changes found in proteins, represented by pairs of ligand-free and ligand-bound structures of identical proteins, and links these changes to ligand-binding.

Platinum is a manually curated, literature-derived database comprising over 1,000 mutations which for the first time associates experimental information on changes in protein-ligand affinity with the three-dimensional structures of the complex.

The STAP database contains refined versions of the NMR structures deposited in PDB. These refinements have been performed using statistical torsion angle potential and structurally- or experimentally- derived distance potential. The refined structure ...

The Telomerase Database is a Web-based tool for the study of structure, function, and evolution of the telomerase ribonucleoprotein. The objective of this database is to serve the research community by providing a comprehensive compilation of informa ...

UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by que ...

SigMol is a specialized repository of quorom sensing signaling molecules (QSSMs) in prokaryotes. SigMol harbors information on QSSMs pertaining to different quorum sensing signaling systems namely acylated homoserine lactones (AHLs), diketopiperazine ...

2P2Idb is a hand-curated structural database dedicated to the modulation of protein-protein interactions (PPIs). It includes all interactions for which both the protein-protein and protein-modulator complexes have been structurally characterized by X ...

The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the lis ...

ccPDB (Compilation and Creation of datasets from PDB) is a collection of commonly used data sets for structural or functional annotation of proteins. There are numerous datasets from the literature and the Protein Data Bank (PDB), which were used for ...

Families of nuclear hormone receptors

Retrotransposons, which comprises LINE, SINE and LTR-containing elements, accounts for almost half of our genome (Fig. 1). They are mobile genetics elements - also known as jumping genes - but only the L1-HS subfamily has retained the ability to jump ...

PDB-REPRDB is a reorganized database of protein chains from PDB(Protein Data Bank), and provides 'the list of the representative protein chains' and 'the list of similar protein chain groups'.

SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.

SCRIPDB is a chemical structure database designed to make patent metadata accessible. We index public-domain chemical information contained in U.S. patents, and provide the full patent text, reactions, and relationships described within any individua ...

Glycan database with focus on carbohydrate 3D structures

VFB is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster. Our goal is to make it easier for researchers to find relevant anatomical information and reagent ...

Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each.

POcket Similarity Search Using Multiple-Sketches (PoSSuM) includes all the discovered protein-small molecule binding site pairs with annotations of various types (e.g., UniProt, CATH, SCOP, SCOPe, EC number and Gene ontology). PoSSuM enables rapid ex ...

T-psi-C is a database of tRNA sequences and 3D tRNA structures. The T-psi-C database can be continuously updated by any member of the scientific community.

ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the ty ...

KnotProt collects information about proteins with knots or slipknots. The knotting complexity of proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The da ...

IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large vari ...

BitterDB is a free and searchable database of bitter compounds. Compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also conta ...

The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant ima ...

The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes.

A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. The TO is part of the Planteome Project.

The Xenopus Anatomical Ontology (XAO) describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. XAO terms describe gene expression, and the ...

The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the "Inhibitor Cystine Knot (ICK) motif/family/fold").

RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repea ...

Evolution of protein-protein Interfaces InterEvol is a resource for researchers to investigate the structural interaction of protein molecules and sequences using a variety of tools and resources.

LinkProt collects information about protein chains and complexes that form links. LinkProt detects deterministic links (with loops closed by cysteine), and determines likelihood of formation of links in networks of protein chains called MacroLinks. L ...

TargetTrack, a target registration database, provides information on the experimental progress and status of targets selected for structure determination.

A structured controlled vocabulary of the anatomy and development of the Zebrafish. If you work on the project responsible for "Zebrafish anatomy and development" then please consider helping us by claiming this record and updating it appropriately.

An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.

PDBselect (http://bioinfo.tg.fh-giessen.de/pdbselect/) is a list of representative protein chains with low mutal sequence identity selected from the protein data bank (PDB) to enable unbiased statistics. The list increased from 155 chains in 1992 to ...

A Database of Hemolytic and Non-hemolytic Peptides

non-B DNA forming motifs in mammalian genomes

ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching ...

Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molec ...

Indel Flanking Region Database is an online resource for indels (insertion/deletions) and the flanking regions of proteins in SCOP superfamilies. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid indels, substitut ...

REFOLDdb is a resource for the optimization of protein refolding, referring to published methods employed in the refolding of recombinant proteins. It stores a collection of published experimental approaches and records for refolding proteins. It con ...

HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb).

Structural data within the Immune Epitope Database

Protein building blocks for structural analysis, modeling and design

Detection of functional divergence in human protein families. Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family class ...

Natural and artificial sweetening agents

3DMET is a database of three-dimensional structures of natural metabolites. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.

SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural para ...

Protein conformation and bond angles and lengths

Protein structures in bound and unbound states

AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. Proteins are frequently associated with other molecules to perform their functions. Experimental structures determined in the bound state are named holo s ...

PSIbase is a molecular interaction database based on PSIMAP (PDB, SCOP) that focuses on structural interaction of proteins and their domains. This resource has been marked as Uncertain because its project home can no longer be found. Please get in to ...

Protein Conformational Diversity database

EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

Hydrogen/deuterium exchange data on protein folding and stability

A public standards-compliant repository for gel-based proteomics data linked to protein identification published in the literature. The repository is continuously extended, putting together a large collection of multi-species reference maps, with tho ...

fPOP (footprinting Pockets Of Proteins) is a database of the protein functional surfaces identified by shape analysis. In this relational database, we collected the spatial patterns of protein binding sites including both holo and apo forms from more ...

Biomolecule Stretching Database

The Open Protein Structure Annotation Network

Database of MacroMolecular INteractions

SNAPPI-DB is an object-oriented database of domain-domain interactions observed in structural data. The structural data is obtained from the MSD data warehouse as the MSD provides consistent data with links to many types of data about proteins and nu ...

Conformational features of DNA

Comprehensive database of fragments linking metabolites, toxic molecules and drugs

SURFACE is a database containing the results of a large-scale protein annotation and local structural comparison project. The homepage of the resource has not been updated since 2003 (and the maintainer's website since 2010). Until we have confirmati ...

Structural Atlas of Human Genome

EK3D - an E. coli K antigen 3-dimensional structure database is a repository of 72 E. coli K antigens that provides information about the sugar composition, epimeric & enantiomeric forms and linkages between the sugar monomers.

PROXiMATE is a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and funct ...

ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properti ...

Dolbico, the Database Of Local Biomolecular Conformers, stores DNA structural data including the information about DNA local spatial arrangement. The main aim of Dolbico is the exploration of DNA structure at a local level. The analysis of local DNA ...

eCrystals is the archive for Crystal Structures generated by the Southampton Chemical Crystallography Group and the EPSRC UK National Crystallography Service. It contains all the fundamental and derived data resulting from a single crystal X-ray stru ...

Binary SubComplexes in Proteins Database

The Pig Genomic Informatics System (PigGIS) presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed ...

Conformation Angles DataBase [ CADB-3.0 ] is a comprehensive, authoritative and timely knowledge base developed to facilitate retrieval of information related to the conformational angles (main-chain and side-chain) of the amino acid residues present ...

Dolce is a database of DNA structure motifs based on an automatic classification method consisting of the combination of supervised and unsupervised approaches. This workflow has been applied to analyze 816 X-ray and 664 NMR DNA structures released t ...

The Blue Star STING database stores information on the interactions between proteins and other bio macromolecules. Structure descriptors used in the analysis of these interactions are stored in STING DB to aid research primarily into the problems cha ...

Protein Topology Graph library: Secondary structure-based protein topologies

Atomistic Molecular Dynamics Simulation Trajectories and Analyses of Nucleic Acid Structures. BIGNASim is a complete platform to hold and analyse nucleic acids simulation data, based on two noSQL database engines: Cassandra to hold trajectory data an ...

LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.

Cereal plant gross anatomy is a structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology.

Plant & Fungal Carbohydrate Structure Database (PFCSDB) stores published data on glycans and glycoconjugates of plant and fungal origin. It provides data on structures, bibliography, taxonomy, 1H and 13C NMR spectrum assignment, methods used for stru ...

Bacterial Carbohydrate Structure Database (BCSDB) stores published data on glycans and glycoconjugates of bacterial and archaean origin. It provides data on structures, bibliography, taxonomy, 1H and 13C NMR spectrum assignment, methods used for stru ...

The SISYPHUS database contains manually curated multiple structural alignments constructed for a set of proteins with known three-dimensional structures that have revealed non-trivial structural relationships and whose structural similarity is ambigu ...

Sequence conservation profiles of the proteins of known structures

DSDBASE is a database of disulphide bonds in proteins that provides information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries. The modelling of disulphides has be ...

Phospho3D is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database als ...

Database of commercially-available compounds for virtual screening and chemoinformatics

Discovery of Broadly Neutralizing Antibodies (bNAbs) has given a great boost to HIV vaccine research. Study of bNAbs capable of neutralizing a broad array of different HIV strains is important for a number of reasons: (i) structures of antigens co-cr ...

Pairwise superposition of TIM-barrel structures

Carbohydrate 3D structures derived from the PDB

Although large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Prediction of the 3D structures of the proteins encoded by sequences provides important clues to their functi ...

HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of r ...

A flat file with CarbBank is vailable for download from this resource: http://www.glycome-db.org/getDownloadPage.action?page=carbbank

Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure

TSTMP is a database designed to help the target selection of human transmembrane proteins for structural genomics projects. The database contains human transmembrane proteins with two or more transmembrane segments considering the existence of an exa ...

Structure-based interface library for macromolecules

Structure Integration with Function, Taxonomy and Sequences

Protein Structure Initiative Structural Genomics Knowledgebase

A resource for elucidating sequence-to-structure relationships for coiled-coil folding and assembly

Alternative Splicing-induced Alteration of Protein Structure

Flexibility in protein structures

Database of Disordered Protein Predictions

Small molecule inhibitors of RNA

DBAli, a database of pairwise and multiple structure alignments, stores pairwise comparisons of all structures in the Protein Data Bank calculated using the program MAMMOTH. It also contains multiple structure alignments generated by the SALIGN comma ...

Evolutionary Classification of Protein Domains

Base interactions in RNA structures

Target data from worldwide structural genomics projects

3D cryo-electron microscopy maps, models and metadata

The circular permutation database

Library of protein family core structures

Automated structural classification of protein sequences

RNA-binding sites database

Database of secondary structures of proteins

RNA structural modules and their interactions

Database of Protein Interaction Sites using multiple binding states in PDB

A database for the computation of atomic packing density values of protein structures

Protein Ensemble Database: ensembles of intrinsically disordered and of unfolded proteins

Structures, iNterfaces and Alignments for Protein-Protein Interactions

Packing of RNA molecules and complexes

The IMB Jena Image Library of Biological Macromolecules (http://www.imb-jena.de/IMAGE.html) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides acces ...

A database housing conformational dynamics data for all the proteins and their biological assemblies from PDB

Structural motifs in protein families and superfamilies

Structural Prediction for pRotein fOlding UTility System

Manual alignments for structurally analogous motifs in proteins

SCOPPI is a database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain associations and are annotated with various in ...

Protein-protein interfaces in co-crystallized protein structures

A database of 3D RNA fragments within known RNA structures

Hot spots (functionally and structurally important residues) in protein interfaces

G-quadruplex motifs and potentially G-quadruplex regulated genes

Prediction of viral microRNA candidate hairpins

Descriptions of protein and macromolecular motions, including movies

The organelle genomes are part of the NCBI Reference Sequence (RefSeq) project that provides curated sequence data and related information for the community to use as a standard.

Decoys are computer generated conformations of protein sequences that possess some characteristics of native proteins, but are not biologically real. The primary use of decoys is to test scoring, or energy, functions.

RNA SSTRAND contains known secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known secondary structures, and to provide the scientific community with simple yet powerful ...

Electrostatic potentials and hydrophobic properties of the active sites

The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath_new) currently contains 34,287 domain structures classified into 1,383 superfamilies and 3,285 sequence families. Each structural family is expanded with domain seq ...

A comprehensive database of toxic compounds

Microbial Volatile Organic Compounds

Carbohydrate database, part of the KEGG system

Database of flavors and scents

KineticDB is a systematically compiled database of protein folding kinetics. The main goal of the KineticDB is to provide users with a diverse set of protein folding rates determined experimentally. At present, the KineticDB contains the results of f ...

Annotated structures of glycan molecules

PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level "virtual" bond and torsion angles, based on their distr ...

PIDD is a dedicated database and structural bio-informatics system for distance based protein modeling. The database is developed to host and analyze the statistical data for protein inter-atomic distances based on their distributions in databases of ...

The Dali database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali se ...

The Protein Folding Database (PFD) is a searchable collection of all annotated structural, methodological, kinetic and thermodynamic data relating to experimental protein folding studies. The database structure allows visualization of folding data in ...

Structural motifs are central to the integrity of the fold and require careful analysis for their identification. IMOTdb is a repertoire of spatially interacting motifs in single protein structures as well as those among distantly related protein str ...

Integral membrane proteins play important roles in living cells. Although these proteins are estimated to constitute around 25% of proteins at a genomic scale, the Protein Data Bank (PDB, http://www.rcsb.org/pdb) contains only a few hundred membrane ...

NPIDB (Nucleic acids – Protein Interaction DataBase) includes a collection of files in the PDB format containing structural information on DNA-protein and RNA-protein complexes, and a number of tools for analysis of those complexes: CluD, a pr ...

Database of glycan 3D structures

RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments

Remote homology detection, namely the accumulation of reliable but distantly related sequences of a protein family, remains a challenging problem in biology. Early realisation of such relationships can provide clues on evolutionary trends and to attr ...

Sting Report is a service for extracting information about an individual amino acid of a protein. This information is presented as a series of GIF images and a table, integrated in a single printer-friendly HTML page, containing values of up to 125 s ...

Database of MacroMolecular INteractions

The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. For selection purposes and for correlation of structural similarity with medical application, the assignment of the Anatomical Therapeutic Chemi ...

Few scientific 3D-printable models are available online, and the expertise required to generate and validate such models remains a barrier. The NIH 3D Print Exchange eliminates this gap with an open, comprehensive, and interactive website for searchi ...

PDB-Ligand is a three dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). One unique feature of PDB-Ligand is that one can browse, classify, superimpose, and visual ...

GRSDB: ‘G’-Rich Sequences DataBase contains information on composition and distribution of putative Quadruplex forming 'G'-Rich Sequences (QGRS) in the alternatively processed (alternatively spliced or alternatively polyadenylated) mamma ...

HIC-Up ("Hetero-compound Information Centre - Uppsala") is a repository of structure-related information about the small molecules (ligands, co-factors, ions, metal-clusters, etc.) that occur in complex with larger biomolecules in any of the structur ...

Proteins can be formed by single or multiple domains. The process of recombination at the molecular level has generated a wide variety of multi-domain proteins with specific domain organization to cater to the functional requirements of an organism. ...

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudoknots. It can be reached by its central page at http://pseudobaseplusplus.utep.edu. From here one can retrieve pseudoknot data as well as submit data fo ...

SARS-CoV RNA SSS DATABASE is a database of the predicted RNA secondary structural sequences of six SARS coronavirus complete genomes which were sequenced and submitted to GenBank by the separate sequencing and research groups from countries and areas ...

STL files describe only the surface geometry of a three-dimensional object without any representation of color, texture or other common CAD model attributes. The STL format specifies both ASCII and binary representations.

GlycoMaps DB is a data base system for the management of conformational maps and profiles, The system allows conformational maps to be archived in a standard format, and it will provide search and comparison facilities. An interface to structures fro ...

The known occurrences of non-canonical base-base interactions in RNA are tabulated in the NCIR (http://prion.bchs.uh.edu/bp_type/) database. Currently, there are over 1700 entries including those from the crystal and NMR structures of RNAs published ...

DSMM is a Database of Simulated Molecular Motions. This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.villa-bosch. ...

Het-PDB Navi is a database that collects small molecules found in Protein Data Bank (PDB). An atomic reality of protein function is based on interactions between a protein and another molecule. One of the approaches to assume protein functions from t ...

ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG). This knowledge environment includes ...