Tag: protein folds and structural domains

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pf ...

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 ...

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of geneti ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

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 ...

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

ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge 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 Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing sta ...

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated Microbial Signal Transduct ...

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 ...

MoonProt Database is a manually curated, searchable, internet-based resource with information about the over 200 proteins that have been experimentally verified to be moonlighting proteins. Moonlighting proteins comprise a class of multifunctional pr ...

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 ...

RNA-binding proteins and their specificities

DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure I ...

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.

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 ...

A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.

Manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.

Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a c ...

Known and predicted protein domain interactions observed in PDB entries,

ADPriboDB is a database of ADP-ribosylated proteins and their literature-identified ADP-ribosylated residues. The database includes a variety of information for each entry, including any drug treatments performed to obtain the identification of the m ...

Predicted secreted bacterial proteins

Protein Common Interface Database

A database of non-interacting proteins

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 ...

Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multiv ...

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 ...

Protein building blocks for structural analysis, modeling and design

Thioester-active enzymes

Domain interaction map: experimental and predicted protein domain interactions

Protein conformation and bond angles and lengths

Protein structures in bound and unbound states

Functional divergence between the subfamilies of a protein domain family

Protein Conformational Diversity database

Polyglutamine Repeats in Proteins

Hydrogen/deuterium exchange data on protein folding and stability

The TransMembrane Protein Helix-Packing Database (TMPad) is an integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins. TMPad includes geometric descriptors of helix ...

Linear motifs in alpha-helical transmembrane proteins

Biomolecule Stretching Database

Database of MacroMolecular INteractions

Somatic mutation hotspots in protein domains in cancer

Structural Atlas of Human Genome

The Lipase Engineering Database (http://www.led.uni-stuttgart.de) integrates information on sequence, structure, and function of lipases, esterases, and related proteins. Sequence data on 806 protein entries are assigned to 38 homologous families, wh ...

SPRITE is a protein structural motif database searching program. Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements of sites and motifs using a graph theoret ...

Projections of protein functional Sites on Exons

Membrane-binding Molecular Recognition Features

Protein Topology Graph library: Secondary structure-based protein topologies

A database to assess the relevance of bacterial genes during host infection. Bacterial Fitness In infecTion dataBase. Host species Any host species Cow (Bos taurus) Chicken (Gallus gallus) Mouse (Mus musculus) Rabbit (Oryctolagus cuniculus) Pig (Su ...

Database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to most structures present in the electron ...

Evolutionary-oriented database of RNA recognition motif sequences.

Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online re ...

A database for eukaryotic peripheral membrane proteins. The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and or lipids, via ...

The evolutionary history of topological variations in the CPA/AT transporters. Structural models, topology information and other details are presented in a searchable database, CPAfold

AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values.

Expansin Engineering Database integrates information on sequence, structure and function of expansins.

Database for membrane protein thermodynamics for understanding folding and stability. MPTherm is a thermodynamic database of membrane proteins and their mutants, contains the thermodynamic data of membrane proteins collected from literature and ProT ...

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 ...

Statistical detection of pathogen-associated protein domains.

Fuzzle 2.0 is a database of evolutionary related protein fragments.

ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.

A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.

ImitateDB is a comprehensive database for information about molecular mimicry candidates represented as DMPs and MMPs for each experimentally validated unique host pathogen protein-protein interaction.

A3D Database is a database for structure-based protein aggregation predictions for the human proteome

AGODB is a comprehensive domain annotation database of argonaute (Ago) proteins, which contains extensive information about 1902 Ago proteins manually extracted from research articles and public databases.

The Animal Proteome Database (AniProtDB) is a comprehensive collection of proteomes from 100 species spanning 21 animal phyla. In addition to providing open access to this collection of high-quality metazoan proteomes, information on predicted protei ...

YPIBP is an inclusive database consisting of all the members of phosphatidylinositols-binding proteins which are collected from high-throughput proteome and lipid array studies, QuickGO and a rigorous literature mining. Cumulatively, across all PI, t ...

The Bacterial Microcompartment Database. MCPdb – The Bacterial Microcompartment Databse. MCPDB A bacterial microcompartment database and structure viewer include Carboxysome Pdu Eut BMC BMV MCP organelle encapsulin protein capsid. MCPdb is an onli ...

Database of amino acid distances in proteins and web application for statistical review of distances. Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interaction ...