Structural database resources for biological macromolecules (Q30389067)

21 June 2017

title

Structural database resources for biological macromolecules (English)

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21 June 2017

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Luciano A Abriata

1

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21 June 2017

publication date

5 June 2016

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Briefings in Bioinformatics

21 June 2017

language of work or name

English

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published in

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Announcing the worldwide Protein Data Bank

21 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Trendspotting in the Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Inference of macromolecular assemblies from crystalline state

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

eF-site and PDBjViewer: database and viewer for protein functional sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Enlarged representative set of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Errors in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The PDB_REDO server for macromolecular structure model optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Detection of trans-cis flips and peptide-plane flips in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

A series of PDB-related databanks for everyday needs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

ChSeq: A database of chameleon sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PCDB: a database of protein conformational diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

CoDNaS: a database of conformational diversity in the native state of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PDBFlex: exploring flexibility in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The use of experimental structures to model protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Protein conformational diversity modulates sequence divergence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

BDB: Databank of PDB files with consistent B-factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

ProDDO: a database of disordered proteins from the Protein Data Bank (PDB).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

MobiDB: a comprehensive database of intrinsic protein disorder annotations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PACSY, a relational database management system for protein structure and chemical shift analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Prediction of the human membrane proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The human transmembrane proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Properties and identification of human protein drug targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Expediting topology data gathering for the TOPDB database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

OPM database and PPM web server: resources for positioning of proteins in membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Anisotropic Solvent Model of the Lipid Bilayer. 2. Energetics of Insertion of Small Molecules, Peptides, and Proteins in Membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The Nucleic Acid Database: new features and capabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

InterRNA: a database of base interactions in RNA structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Identifying novel sequence variants of RNA 3D motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

RNA Bricks--a database of RNA 3D motifs and their interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The importance of dynamics in integrative modeling of supramolecular assemblies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

An updated version of NPIDB includes new classifications of DNA-protein complexes and their families.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

sc-PDB: a 3D-database of ligandable binding sites--10 years on

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Pocketome: an encyclopedia of small-molecule binding sites in 4D

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PeptiSite: a structural database of peptide binding sites in 4D.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PDTD: a web-accessible protein database for drug target identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

TarFisDock: a web server for identifying drug targets with docking approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

KLIFS: a structural kinase-ligand interaction database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Antigen–Antibody Interaction Database (AgAbDb): A Compendium of Antigen–Antibody Interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Metalloproteomes: a bioinformatic approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Structural biology of the lanthanides-mining rare earths in the Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Analysis of copper–ligand bond lengths in X-ray structures of different types of copper sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

A less-biased analysis of metalloproteins reveals novel zinc coordination geometries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Small revisions to predicted distances around metal sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Automated identification of elemental ions in macromolecular crystal structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

MetalPDB: a database of metal sites in biological macromolecular structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

MINAS--a database of Metal Ions in Nucleic AcidS

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

pKNOT v.2: the protein KNOT web server

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

RepeatsDB: a database of tandem repeat protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

ArchDB 2014: structural classification of loops in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Decoding the Mobility and Time Scales of Protein Loops

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Glycan fragment database: a database of PDB-based glycan 3D structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

Molecular Dynamics Simulations of Glycoproteins Using CHARMM

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

UbSRD: The Ubiquitin Structural Relational Database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

SATPdb: a database of structurally annotated therapeutic peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

EMDataBank unified data resource for 3DEM.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The Uppsala Electron-Density Server

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

ChEBI in 2016: Improved services and an expanding collection of metabolites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

ChEMBL web services: streamlining access to drug discovery data and utilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

The Chemical Space Project

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

PubChem Substance and Compound databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

HMDB 3.0--The Human Metabolome Database in 2013

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

ZINC--a free database of commercially available compounds for virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBW049

21 January 2018

Identifiers

DOI

10.1093/BIB/BBW049

0 references

DBLP publication ID

journals/bib/Abriata17

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference