Cargando…

Homology‐based hydrogen bond information improves crystallographic structures in the PDB

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimize...

Descripción completa

Detalles Bibliográficos
Autores principales:	van Beusekom, Bart, Touw, Wouter G., Tatineni, Mahidhar, Somani, Sandeep, Rajagopal, Gunaretnam, Luo, Jinquan, Gilliland, Gary L., Perrakis, Anastassis, Joosten, Robbie P.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	John Wiley and Sons Inc. 2017
Materias:	Tools for Protein Science
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5818736/ https://www.ncbi.nlm.nih.gov/pubmed/29168245 http://dx.doi.org/10.1002/pro.3353

Ejemplares similares

Homology-based loop modeling yields more complete crystallographic protein structures
por: van Beusekom, Bart, et al.
Publicado: (2018)

Facilities that make the PDB data collection more powerful
por: Lange, Joanna, 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)

PDBsum: Structural summaries of PDB entries
por: Laskowski, Roman A., et al.
Publicado: (2017)

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank
por: Joosten, Robbie P., et al.
Publicado: (2011)

ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins
por: Ben Chorin, Adi, et al.
Publicado: (2019)

CC(+) : A searchable database of validated coiled coils in PDB structures and AlphaFold2 models
por: Kumar, Prasun, et al.
Publicado: (2023)

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

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

LAHMA: structure analysis through local annotation of homology-matched amino acids
por: van Beusekom, Bart, et al.
Publicado: (2021)

Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data
por: Casañal, Ana, et al.
Publicado: (2020)

A series of PDB-related databanks for everyday needs
por: Touw, Wouter G., et al.
Publicado: (2014)

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

A knowledge-driven approach for crystallographic protein model completion
por: Joosten, Krista, et al.
Publicado: (2008)

Building and rebuilding N-glycans in protein structure models
por: van Beusekom, Bart, 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-tools: a swiss army knife for molecular structures
por: Rodrigues, João P. G. L. M., et al.
Publicado: (2018)

A crystal structure of the human protein kinase Mps1 reveals an ordered conformation of the activation loop
por: Roorda, Jacomina C., et al.
Publicado: (2019)

Timely deposition of macromolecular structures is necessary for peer review
por: Joosten, Robbie P., et al.
Publicado: (2013)

AlphaFill: enriching AlphaFold models with ligands and cofactors
por: Hekkelman, Maarten L., et al.
Publicado: (2022)

The Geminin and Idas Coiled Coils Preferentially Form a Heterodimer That Inhibits Geminin Function in DNA Replication Licensing
por: Caillat, Christophe, et al.
Publicado: (2013)

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

A New Generation of Crystallographic Validation Tools for the Protein Data Bank
por: Read, Randy J., et al.
Publicado: (2011)

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

Elucidation of Single Hydrogen Bonds in GTPases via Experimental and Theoretical Infrared Spectroscopy
por: Mann, Daniel, et al.
Publicado: (2017)

One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor
por: Zhou, Beifei, et al.
Publicado: (2017)

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

Automating tasks in protein structure determination with the clipper python module
por: McNicholas, Stuart, et al.
Publicado: (2017)

CCBuilder 2.0: Powerful and accessible coiled‐coil modeling
por: Wood, Christopher W., et al.
Publicado: (2017)

OPUS‐CSF: A C‐atom‐based scoring function for ranking protein structural models
por: Xu, Gang, et al.
Publicado: (2017)

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education
por: Burley, Stephen K., et al.
Publicado: (2017)

DichroMatch at the protein circular dichroism data bank (DM@PCDDB): A web‐based tool for identifying protein nearest neighbors using circular dichroism spectroscopy
por: Whitmore, Lee, et al.
Publicado: (2017)

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
por: Kinjo, Akira R., et al.
Publicado: (2017)

Functional classification of protein structures by local structure matching in graph representation
por: Mills, Caitlyn L., et al.
Publicado: (2018)

ProtaBank: A repository for protein design and engineering data
por: Wang, Connie Y., et al.
Publicado: (2018)

CDtoolX, a downloadable software package for processing and analyses of circular dichroism spectroscopic data
por: Miles, Andrew J., et al.
Publicado: (2018)

Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models
por: Brzezinski, Dariusz, et al.
Publicado: (2020)

PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system
por: Schiffrin, Bob, et al.
Publicado: (2020)

The Dundee Resource for Sequence Analysis and Structure Prediction
por: MacGowan, Stuart A., et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_osliqhvbtks8rth3ogc1srneo2