Tag: structure analysis


Found 35 sources
Source Match ReputationScore*

Protein Data Bank Japan


The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
100%

PDB_REDO databank


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 ...
94%

Molecular Modeling Database


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.
93%

Phospho.ELM


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.
93%

PASS2


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 ...
91%

GlycomeDB


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.
85%

ValidatorDB


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 ...
84%

WHAT IF


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 ...
81%

FunTree: A Resource For Exploring The Functional Evolution Of Structurally Defined Enzyme Superfamilies


A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.
80%

Electron density server at Uppsala university


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 ...
78%

Statistical Torsional Angles Potentials of NMR Refinement Database


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 ...
77%

Protein Model Portal


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 ...
76%

Autophagy Database


Proteins involved in self-digestion of eukaryotic cells
76%

EMDataBank.org


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 ...
75%

InterEvol database : Diving into the structure and evolution of protein complex interfaces


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.
73%

Allosteric Database


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 ...
72%

MimoDB


Mimotope database, active site-mimicking peptides selected from phage-display libraries
72%

PepX


A non-redundant database of protein-peptide complexes
71%

non-B DB


non-B DNA forming motifs in mammalian genomes
71%

MolMovDB


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.
71%

3D-Footprint


Estimates of DNA-binding specificity for protein-DNA complexes in PDB
70%

OMPdb


Beta-barrel outer membrane proteins from Gram-negative bacteria
69%

IEDB-3D


Structural data within the Immune Epitope Database
69%

MetaBase


Wiki database of biological databases
67%

fPOP


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 ...
65%

RIKEN mammals


Integrated database of mammalian genomes, phenotypes, strains and cell lines
65%

3DNALandscapes


Conformational features of DNA
65%

EDULISS


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 ...
61%

SwissSidechain


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.
55%

QSbio


A dataset of conserved quaternary structure (QS) across Protein Data Ban (PDB).
51%

SkinSensDB


Curated database for skin sensitization assays.
51%

Click2Drug


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 ...
51%

TiPs


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 ...
51%

M-IOLITE


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 ...
51%

PDB-REDO databank of optimised macromolecular structures


Databank of optimised macromolecular structures. PDB-REDO entries are refined, rebuilt and validated with one consistent protocol using the equivalent entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically have higher st ...
51%

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