Cargando…

A series of PDB-related databanks for everyday needs

We present a series of databanks (http://swift.cmbi.ru.nl/gv/facilities/) that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run parallel to the PDB, i.e. they have one entry per...

Descripción completa

Detalles Bibliográficos
Autores principales:	Touw, Wouter G., Baakman, Coos, Black, Jon, te Beek, Tim A. H., Krieger, E., Joosten, Robbie P., Vriend, Gert
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Database Issue
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383885/ https://www.ncbi.nlm.nih.gov/pubmed/25352545 http://dx.doi.org/10.1093/nar/gku1028

Ejemplares similares

A series of PDB related databases for everyday needs
por: Joosten, Robbie P., et al.
Publicado: (2011)

Facilities that make the PDB data collection more powerful
por: Lange, Joanna, et al.
Publicado: (2019)

Homology modelling and spectroscopy, a never-ending love story
por: Venselaar, Hanka, et al.
Publicado: (2009)

PDBe: improved findability of macromolecular structure data in the PDB
por: Armstrong, David R, et al.
Publicado: (2020)

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB
por: Velankar, Sameer, et al.
Publicado: (2016)

MetalPDB in 2018: a database of metal sites in biological macromolecular structures
por: Putignano, Valeria, et al.
Publicado: (2018)

CovPDB: a high-resolution coverage of the covalent protein–ligand interactome
por: Gao, Mingjie, et al.
Publicado: (2021)

sc-PDB: a 3D-database of ligandable binding sites—10 years on
por: Desaphy, Jérémy, et al.
Publicado: (2014)

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
por: Joosten, Robbie P., et al.
Publicado: (2009)

Detection of trans–cis flips and peptide-plane flips in protein structures
por: Touw, Wouter G., et al.
Publicado: (2015)

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein–protein interaction sites for PDB structures
por: Ripoche, Hugues, et al.
Publicado: (2017)

The Meaning of Neurotrauma Databank
por: Yun, Gi Yong, et al.
Publicado: (2022)

QSAR DataBank repository: open and linked qualitative and quantitative structure–activity relationship models
por: Ruusmann, V, et al.
Publicado: (2015)

Homology‐based hydrogen bond information improves crystallographic structures in the PDB
por: van Beusekom, Bart, et al.
Publicado: (2017)

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
por: Burley, Stephen K, et al.
Publicado: (2022)

Cancer Odor Database (COD): a critical databank for cancer diagnosis research
por: Janfaza, Sajjad, et al.
Publicado: (2017)

PDB_REDO: automated re-refinement of X-ray structure models in the PDB
por: Joosten, Robbie P., et al.
Publicado: (2009)

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics
por: von Grotthuss, Marcin, et al.
Publicado: (2006)

ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements
por: Vignesh, Dhandapani, et al.
Publicado: (2010)

GPCRdb: an information system for G protein-coupled receptors
por: Isberg, Vignir, et al.
Publicado: (2016)

iPPI-DB: an online database of modulators of protein–protein interactions
por: Labbé, Céline M., et al.
Publicado: (2016)

Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins
por: Hsing, Michael, et al.
Publicado: (2008)

AntiTbPdb: a knowledgebase of anti-tubercular peptides
por: Usmani, Salman Sadullah, et al.
Publicado: (2018)

Correcting ligands, metabolites, and pathways
por: Ott, Martin A, et al.
Publicado: (2006)

Validation and correction of Zn–Cys(x)His(y) complexes
por: Touw, Wouter G., et al.
Publicado: (2016)

MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains
por: Wiel, Laurens, et al.
Publicado: (2019)

CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea
por: Tang, Zhongjie, et al.
Publicado: (2019)

PDB_REDO: constructive validation, more than just looking for errors
por: Joosten, Robbie P., et al.
Publicado: (2012)

The PDB_REDO server for macromolecular structure model optimization
por: Joosten, Robbie P., et al.
Publicado: (2014)

Making glycoproteins a little bit sweeter with PDB-REDO
por: van Beusekom, Bart, et al.
Publicado: (2018)

GPCRDB: information system for G protein-coupled receptors
por: Vroling, Bas, et al.
Publicado: (2011)

ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank
por: Agrawal, Piyush, et al.
Publicado: (2019)

MetaboLights: a resource evolving in response to the needs of its scientific community
por: Haug, Kenneth, et al.
Publicado: (2020)

On the complexity of Engh and Huber refinement restraints: the angle τ as example
por: Touw, Wouter G., et al.
Publicado: (2010)

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
por: Kinjo, Akira R., et al.
Publicado: (2017)

Tools and data services registry: a community effort to document bioinformatics resources
por: Ison, Jon, et al.
Publicado: (2016)

piRTarBase: a database of piRNA targeting sites and their roles in gene regulation
por: Wu, Wei-Sheng, et al.
Publicado: (2019)

dbMAE: the database of autosomal monoallelic expression
por: Savova, Virginia, et al.
Publicado: (2016)

New restraints and validation approaches for nucleic acid structures in PDB-REDO
por: de Vries, Ida, et al.
Publicado: (2021)

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
por: Hornbeck, Peter V., et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_0744gni1pehkfldl9cj5anuq80