Protein Data Bank Japan
Names
More detailed information about this field from each metasource.
Protein Data Bank Japan
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
PDBj
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
pdbj
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
Names
More detailed information about this field from each metasource.
Protein Data Bank Japan
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
PDBj
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
pdbj
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:15.091732
Names
More detailed information about this field from each metasource.
Protein Data Bank Japan
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
PDBj
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
pdbj
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:15.091732
The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
Description
More detailed information about this field from each metasource.
The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
PDBj (Protein Data Bank Japan) provides a centralized PDB archive of macromolecular structures, integrated tools for data retrieval, visualization, and functional characterization. PDBj is supported by JST-NBDC and Osaka University.
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
Protein Data Bank Japan: a member of the worldwide Protein Data Bank (wwPDB), accepts and processes desposited data of experimentally determinded macromolecular structures.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:15.091732
Webpage:
http://www.pdbj.org/Webpage
More detailed information about this field from each metasource.
http://www.pdbj.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://pdbj.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
https://pdbj.org/
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
Licence:
Name: PDBJ Attribution requiredLicence name
More detailed information about this field from each metasource.
PDBJ Attribution required
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
other
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
Licence URL
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https://pdbj.org/info/terms-conditions
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://www.wwpdb.org/about/agreement
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
Publications:
(7)
Publications
More detailed information about this field from each metasource.
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
PMID: 21976737
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
PMID: 27789697
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
PMID: 28815765
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
PMID: 20798081
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
[Development of PDBj: Advanced database for protein structures]
PMID: 12099029
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr
PMID: 21796434
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/GKR811
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
PMID: 21976737
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
PMID: 27789697
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
PMID: 28815765
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
PMID: 20798081
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
[Development of PDBj: Advanced database for protein structures]
PMID: 12099029
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr
PMID: 21796434
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/GKR811
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
PubMed citations: 62.
62 articles citing: Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
Computational Study on the Dynamics of Mycobacterium Tuberculosis RNA Polymerase Assembly. PMID:35922622
The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science. PMID:35480260
Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin. PMID:35207496
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. PMID:34664328
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
The Protein Data Bank Archive. PMID:33950382
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. PMID:32512182
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Beyond Fever and Pain: Diagnostic Methods for Chikungunya Virus. PMID:30995993
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
BioSearch: a semantic search engine for Bio2RDF. PMID:29220451
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
Decoding disease-causing mechanisms of missense mutations from supramolecular structures. PMID:28819267
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). PMID:28815765
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
Learning from biomedical linked data to suggest valid pharmacogenes. PMID:28427468
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
Protein Bioinformatics Databases and Resources. PMID:28150231
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. PMID:27927232
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. PMID:27794042
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. PMID:27789697
Molmil: a molecular viewer for the PDB and beyond. PMID:27570544
LigandBox: A database for 3D structures of chemical compounds. PMID:27493549
GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. PMID:27493524
Getting the most out of PubChem for virtual screening. PMID:27454129
The archiving and dissemination of biological structure data. PMID:27450113
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
DCC: a Swiss army knife for structure factor analysis and validation. PMID:27275151
The FAIR Guiding Principles for scientific data management and stewardship. PMID:26978244
High-Density Peptide Microarray Analysis of IgG Autoantibody Reactivities in Serum and Cerebrospinal Fluid of Multiple Sclerosis Patients. PMID:26831522
Automatic generation of bioinformatics tools for predicting protein-ligand binding sites. PMID:26545824
A novel loss-of-function mutation of GATA3 (p.R299Q) in a Japanese family with Hypoparathyroidism, Deafness, and Renal Dysplasia (HDR) syndrome. PMID:26514990
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. PMID:26508754
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
PubChem Substance and Compound databases. PMID:26400175
Implementation of linked data in the life sciences at BioHackathon 2011. PMID:25973165
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. PMID:25540181
Protein structure annotation resources. PMID:25502191
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
Small molecule annotation for the Protein Data Bank. PMID:25425036
EzCatDB: the enzyme reaction database, 2015 update. PMID:25324316
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. PMID:25089180
The Protein Data Bank archive as an open data resource. PMID:25062767
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. PMID:24829452
Toolboxes for a standardised and systematic study of glycans. PMID:24564482
Chemical annotation of small and peptide-like molecules at the Protein Data Bank. PMID:24291661
PDBe: Protein Data Bank in Europe. PMID:24288376
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. PMID:24113529
How community has shaped the Protein Data Bank. PMID:24010707
An overview of tools for the validation of protein NMR structures. PMID:23877928
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
Trendspotting in the Protein Data Bank. PMID:23337870
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. PMID:23180575
The future of the Protein Data Bank. PMID:23023942
Creating a community resource for protein science. PMID:22969036
Public domain databases for medicinal chemistry. PMID:22731701
PDBe: Protein Data Bank in Europe. PMID:22110033 -
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
PubMed citations: 43.
43 articles citing: Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
Metnase and EEPD1: DNA Repair Functions and Potential Targets in Cancer Therapy. PMID:35155245
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins. PMID:34745807
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. PMID:34664328
Autoencoder-based detection of the residues involved in G protein-coupled receptor signaling. PMID:34615896
virusMED: an atlas of hotspots of viral proteins. PMID:34614039
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. PMID:34506132
Regulatory properties of vitronectin and its glycosylation in collagen fibril formation and collagen-degrading enzyme cathepsin K activity. PMID:34103584
Machine learning enabled identification of potential SARS-CoV-2 3CLpro inhibitors based on fixed molecular fingerprints and Graph-CNN neural representations. PMID:34052441
Rifampicin and Letermovir as potential repurposed drug candidate for COVID-19 treatment: insights from an in-silico study. PMID:33970450
Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level. PMID:33759128
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations. PMID:33658550
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19. PMID:32983399
On the evolution of the quality of macromolecular models in the PDB. PMID:32311227
Impact of the Protein Data Bank on antineoplastic approvals. PMID:32068073
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations. PMID:32026396
Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations. PMID:31996730
All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins. PMID:31984182
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
Loosening of Side-Chain Packing Associated with Perturbations in Peripheral Dynamics Induced by the D76N Mutation of β2-Microglobulin Revealed by Pressure-NMR and Molecular Dynamic Simulations. PMID:31527472
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. PMID:31114881
Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity. PMID:30945220
Anticipating innovations in structural biology. PMID:30912485
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. PMID:30595456
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. PMID:30532050
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
Thermal stability of single-domain antibodies estimated by molecular dynamics simulations. PMID:30394618
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. PMID:30090808
Evaluation of variability in high-resolution protein structures by global distance scoring. PMID:29560428
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Validation of Structures in the Protein Data Bank. PMID:29174494
Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank. PMID:29103094
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment. PMID:28828285
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). PMID:28815765
MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures. PMID:28574982 -
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
PubMed citations: 28.
28 articles citing: New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
Insights into Binding of Single-Stranded Viral RNA Template to the Replication-Transcription Complex of SARS-CoV-2 for the Priming Reaction from Molecular Dynamics Simulations. PMID:35199520
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens. PMID:34739839
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. PMID:34664328
PDB-101: Educational resources supporting molecular explorations through biology and medicine. PMID:34601771
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. PMID:34506132
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. PMID:34301175
PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences. PMID:34228733
Machine learning enabled identification of potential SARS-CoV-2 3CLpro inhibitors based on fixed molecular fingerprints and Graph-CNN neural representations. PMID:34052441
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
The Protein Data Bank Archive. PMID:33950382
Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level. PMID:33759128
Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations. PMID:33658550
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans. PMID:33098466
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PMID:33075050
An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19. PMID:32983399
On the evolution of the quality of macromolecular models in the PDB. PMID:32311227
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations. PMID:32026396
Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations. PMID:31996730
All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins. PMID:31984182
Dynamic properties of oligomers that characterize low-frequency normal modes. PMID:31984175
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins. PMID:30923664
Thermal stability of single-domain antibodies estimated by molecular dynamics simulations. PMID:30394618
Meeting Report of the International Life Science Integration Workshop 2018. PMID:29982395 -
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
PubMed citations: 11.
11 articles citing: PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin. PMID:35207496
Glycoinformatics Tools for Comprehensive Characterization of Glycans Enzymatically Released from Proteins. PMID:34611862
Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models. PMID:32981130
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). PMID:28815765
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. PMID:27789697
GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. PMID:27493524
Protein structure annotation resources. PMID:25502191
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. PMID:22139937
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. PMID:21976737
Graphical representation and mathematical characterization of protein sequences and applications to viral proteins. PMID:21570664 -
[Development of PDBj: Advanced database for protein structures]
PubMed citations: 3.
3 articles citing: [Development of PDBj: Advanced database for protein structures]
Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. PMID:33984281
The data universe of structural biology. PMID:32695409
Graphical representation and mathematical characterization of protein sequences and applications to viral proteins. PMID:21570664 -
Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr
PubMed citations: 1.
1 articles citing: Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr
An interview with Phil Bourne, associate director of the RCSB protein data bank. PMID:22366956 - http://dx.doi.org/10.1093/nar/GKR811
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function analysis
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
covid-19
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
biology
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
molecular biology
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
proteomics
metasource: re3data.org
version: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
ontology and terminology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
protein structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
structural biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
Tags
More detailed information about this field from each metasource.
function analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: Protein Data Bank Japan; Protein Data Bank Japan; DOI: https://doi.org/10.25504/FAIRsharing.rs2815; Last edited: April 26, 2021, 2:49 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
covid-19
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
biology
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
molecular biology
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.091732
proteomics
metasource: re3data.orgversion: re3data.org: PDBj; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RP75 last accessed: 2022-11-04
ontology and terminology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:15.091732
structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:15.091732
protein structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:15.091732
structural biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:15.091732
function analysis molecular structure protein structure structure protein structure covid-19 molecular biology proteins proteomics ontology and terminology structure analysis protein structure analysis structural biology
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