Tag: structure analysis

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

The PDB_REDO databank contains alternative (in many cases higher quality) versions of Protein Data Bank (PDB) structure models that were optimised by model refinement and rebuilding. The structure models are supplemented by validation data that desc ...

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.

Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets.

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 ...

PDB-REDO is a databank of optimised (re-refined, rebuilt and validated) Protein Data Bank entries. It covers nearly all structure models derived from X-ray and electron diffraction that have deposited experimental data. Entries can be accessed by the ...

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.

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 ...

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 ...

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

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 ...

A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are p ...

Proteins involved in self-digestion of eukaryotic cells

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 ...

EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB ...

Allostery is the most direct and efficient way for regulation of biological macromolecule function induced by the binding of a ligand at an allosteric site topographically distinct from the orthosteric site. Due to the inherent high receptor selectiv ...

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.

Mimotope database, active site-mimicking peptides selected from phage-display libraries

A non-redundant database of protein-peptide complexes

non-B DNA forming motifs in mammalian genomes

The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.

Estimates of DNA-binding specificity for protein-DNA complexes in PDB

Beta-barrel outer membrane proteins from Gram-negative bacteria

Structural data within the Immune Epitope Database

Wiki database of biological databases

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 ...

Integrated database of mammalian genomes, phenotypes, strains and cell lines

Conformational features of DNA

Database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for uniq ...

SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.

A dataset of conserved quaternary structure (QS) across Protein Data Ban (PDB).

Curated database for skin sensitization assays.

Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free en ...

This database collects predicted drug targets in 150 pathogen species. The structural details of the drug mode of binding are also provided. Predictions are made using the information coming from drug-target three-dimensional complexes and by exploit ...

MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems ...