Tag: protein structure analysis

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 ...

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic ...

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 ...

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

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 ...

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 ...

Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS) is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and c ...

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 ...

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

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 ...

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 ...

PDB Related Datbases present a series of databases that run parallel to the PDB. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all p ...

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 ...

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 ...

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 ...

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 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 ...

Protein Conformational Diversity database

The Open Protein Structure Annotation Network

A database of interactors and mutations of the human von Hippel-Lindau tumor suppressor protein (pVHL).

The Protein Ensemble Database (PED) is an open access database for the deposition of structural ensembles including intrinsically disordered proteins

Protein Topology Graph library: Secondary structure-based protein topologies

SCEptRe provides weekly updated, non-redundant, user customized benchmark datasets with information on the immune receptor features for receptor-specific epitope predictions. This tool extracts weekly updated 3D complexes of antibody-antigen, TCR-pMH ...

A database-integration approach for protein/genome information retrieval.

A multi-step approach including models’ construction (multiple sequence alignment, homology modeling), complex assembling (protein complex refinement with HADDOCK and complex equilibration), and protein-protein interface (PPI) characterization (inclu ...

DbStRiPs (Database of structural repeats in proteins) is a structural repeat database which classifies a protein structure into a structural repeat family based on graph based structural repeat identification algorithm, PRIGSA2.

ViroidDB is the most comprehensive collection of viroid, satellite RNA, retrozyme, and deltavirus genome sequences available on the internet.

Experimental coronavirus protein structures

Database of human missense variants mapped to 3D protein structures.

The database revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. It contains a systematic analysis of all phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein ...

CoDNaS Quaternary is a high confidence database of conformational diversity in proteins that present a biologically relevant quaternary structure.

A database that collects tetrads, quadruplexes, and G4-helices found in PDB-deposited structures of nucleic acids. It stores their sequences, secondary and tertiary structures, and motif-specific description including planarity, rise and twist parame ...