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wwPDB: Worldwide Protein Data Bank

Manage the wwPDB Core Archives as a public good according to the FAIR Principles. Provide expert deposition, validation, biocuration, and remediation services at no charge to Data Depositors worldwide. Ensure universal open access to public domain...

http://www.wwpdb.org/ 

Worldwide Protein Data Bank - Wikipedia

The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly availa...

https://en.wikipedia.org/wiki/Worldw... 

wwPDB: Celebrating 50 Years of the Protein Data Bank Archive

wwPDB: Celebrating 50 Years of the Protein Data Bank Archive Celebrating 50 Years of the Protein Data Bank Archive In 1971, the structural biology community established the single worldwide archive for macromolecular structure data–the Protein D...

https://www.wwpdb.org/pdb50 

wwPDB Foundation

Contact. Worldwide Protein Data Bank Foundation 174 Frelinghuysen Rd | Piscataway, NJ 08854-8076 [email protected]

https://foundation.wwpdb.org/pdb50.h... 

RCSB PDB: Homepage

May 04, 2021  · As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches ba...

https://www.rcsb.org/ 

Worldwide Protein Data Bank - Wikipedia

Worldwide Protein Data Bank - Wikipedia

https://en.wikipedia.org/wiki/Worldw... 

Worldwide Protein Data Bank - Wikipedia

Worldwide Protein Data Bank - Wikipedia

https://en.wikipedia.org/wiki/Worldw... 

Protein Data Bank - Wikipedia

Protein Data Bank - Wikipedia

https://en.wikipedia.org/wiki/Protei... 

wwPDB Validation Service - wwPDB OneDep System

wwPDB Validation Service - wwPDB OneDep System

https://validate-rcsb-1.wwpdb.org/ 

wwPDB Validation Service

Welcome to the wwPDB validation system! This server runs the performs the same validation as you would observe during the deposition process. This service is designed to help you check your model and experimental files prior to start of deposition...

https://validate-rcsb-1.wwpdb.org/ 

pdbml.wwpdb.org - PDBML Schema Resources

This schema is produced by direct translation of the PDBx/mmCIF Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. Data files in...

https://pdbml.wwpdb.org/ 

PDB - FTP Archive over HTTP

For more information about PDB file downloads please see the wwPDB website.wwPDB website.

https://ftp.wwpdb.org/ 

wwPDB Foundation

wwPDB Foundation The wwPDB Foundation is grateful for the efforts of our individual and industrial sponsors. To support the wwPDB Foundation and the PDB50 celebrations, please contact Christine Zardecki or donate via PayPal: 2021 Industrial Sponso...

https://foundation.wwpdb.org/donatio... 

wwPDB: Depositions

The wwPDB deposition system at Rutgers University is currently unavailable. During this time, you will not be able to access existing deposition sessions. You will shortly be able to continue in progress depositions by returning to https://deposit...

https://deposit-4.wwpdb.org/ 

PDB-Dev

Feb 09, 2018  · The structural models obtained through integrative modeling are collected, archived and disseminated to the public through PDB-Dev. Once the mechanisms for processing integrative models are fully established through ...

https://pdb-dev.wwpdb.org/ 

PDB Extract PDB to mmCIF conversion service

PDB Extract converts PDB format file to mmCIF format file for structural models of proteins, nucleic acids, or macromolecular complexes. The output mmCIF format file can be directly used for deposition to wwPDB OneDep system. For models resolved b...

https://pdb-extract.wwpdb.org/ 

PDB-Dev | Login

Please note that experimental structures determined using X-ray crystallography or NMR spectroscopy or Electron microscopy should be deposited through the wwpdb OneDep system.. Purely computational models obtained using homology modeling or ab ini...

https://deposit.pdb-dev.wwpdb.org/ac... 

PDB-Dev

PDB-Dev is a prototype deposition and archiving system for structural models obtained using integrative or hybrid modeling. Structures of complex macromolecular assemblies are increasingly determined using integrative modeling, where a combination...

https://pdb-dev.wwpdb.org/about.html 

wwPDB Tools — ProDy

Mar 11, 2021  · wwPDB Tools¶. This module defines functions for accessing wwPDB servers. wwPDBServer (*key) [source] ¶. Set/get wwPDB FTP/HTTP server location used for downloading PDB structures. Use one of the following k...

http://prody.csb.pitt.edu/manual/ref... 

Dictionary Index mmcif_pdbx.dic

Aug 21, 2012  · wwPDB Dictionary maintainers wwPDB Dictionary name mmcif_pdbx.dic Dictionary version 5.342 Last update 2021-04-19. Downloads . Dictionary Text Dictionary Text (gz) Dictionary Revision History . View/Hide revision his...

https://mmcif.wwpdb.org/dictionaries... 

5 Easy Steps to PDB Deposition with OneDep

Visit pdb-extract.wwpdb.org • Creates single PDBx/ mmCIF file containing extra meta data (e.g., author info, data collection and refinement stats) using output log files • Converts SF files to PDBx/ mmCIF format for non-MTZ format files Attemp...

https://cdn.rcsb.org/wwpdb/docs/depo... 

wwPDB: Advisory Committee

Sep 27, 2013  · wwPDB Advisory Committee Meetings. The wwPDBAC is made up of an international team of experts in X-ray crystallography, cryoEM, NMR, and bioinformatics. The team meets annually. October 18, 2019 (Osaka, Japan)

http://remediation.wwpdb.org/wwpdbac... 

pdb_extract Tutorial

wwPDB: Worldwide Protein Data Bank. Step-by-step Instructions for using the pdb_extract webserver. pdb_extract can be used to convert PDB format files to PDBx/mmCIF format and is a vital resource for the submission of large structures.

https://pdb-extract.wwpdb.org/tutori... 

Announcing the worldwide Protein Data Bank | Nature ...

Dec 01, 2003  · The wwPDB recognizes the importance of providing equal access to the database—both in terms of depositing and retrieving data—from different regions of the world.

https://www.nature.com/articles/nsb1... 

Protein Data Bank - Wikipedia

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-e...

https://en.wikipedia.org/wiki/Protei... 

Worldwide PDB - Home | Facebook

Worldwide PDB. 2.1K likes. wwPDB manages the PDB archive, the authoritative global resource for experimentally determined 3D structures of important biological macromolecules.

https://www.facebook.com/wwPDB/?__xt... 

SF-Tool

SF-tool is to used to (1) convert various structure factor fromats, (2) perform validation of structure factors against model.

http://sf-tool.wwpdb.org/ 

PDB - FTP Archive over HTTP - ftp.wwpdb.org

For more information about PDB file downloads please see the wwPDB website.wwPDB website.

https://ftp.wwpdb.org/pub/pdb/valida... 

Protein Data Bank (PDB): The Single Global Macromolecular ...

The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currentl...

https://pubmed.ncbi.nlm.nih.gov/2857... 

Protein Data Bank: the single global archive for 3D ...

To improve consistency of data within the PDB Core archive, wwPDB biocurators routinely update PDB entries with new or corrected metadata, such as citation information or updates triggered by changes to the CCD (30). The wwPDB has undertaken sever...

https://academic.oup.com/nar/article... 

Worldwide PDB - Home | Facebook

Worldwide PDB. 2.2K likes. wwPDB manages the PDB archive, the authoritative global resource for experimentally determined 3D structures of important biological macromolecules.

https://www.facebook.com/wwPDB/?_ft_... 

wwpdb.utils.ws-utils · PyPI

Dec 30, 2020  · Hashes for wwpdb.utils.ws_utils-0.4.1.tar.gz; Algorithm Hash digest; SHA256: 18260aaf8e6ecadc1f0f14b8c914e177732ad09d4d060459e84155d8c9f06129: Copy MD5

https://pypi.org/project/wwpdb.utils... 

Full wwPDB EM Validation Report O i

Page 8 ullF wwPDB EM alidationV Report EMD-11994, 7B3C 5 Model quality O i 5.1 Standard geometry O i Bond lengths and bond angles in the following residue types are not alidatedv in this section: ZN, F86 The Z score for a bond length (or angle) is...

https://files.rcsb.org/pub/pdb/valid... 

deposit.wwpdb.org EASY q Refer to UniProt STEPS TO PDB

The wwPDB provides a standalone validation server for checking your structure Visit validate.wwpdb.org Both model and experi-mental data are validated Provides detailed reports (PDF and XML files) Query 61 RWWANDGRTPGSR RWW NDGRTPGSR 79 RWWCNDGRTP...

https://cdn.rcsb.org/wwpdb/docs/depo... 

wwPDB biocuration: on the front line of structural biology

wwPDB biocuration: on the front line of structural biology Nat Methods. 2021 May;18(5):431-432. doi: 10.1038/s41592-021-01137-z. Authors Jasmine Y Young 1 , John Berrisford 2 , Minyu Chen 3 Affiliations 1 Research Collaboratory for Structural Bioi...

https://pubmed.ncbi.nlm.nih.gov/3396... 

worldwide Protein Data Bank (wwPDB) - YouTube

The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. Members are:...

https://www.youtube.com/channel/UCgM... 

wwpdb.utils.config · PyPI

Jan 25, 2021  · Files for wwpdb.utils.config, version 0.22.3; Filename, size File type Python version Upload date Hashes; Filename, size wwpdb.utils.config-0.22.3-py2.py3-none-any.whl (39.6 kB) File type Wheel Python version py2.py3...

https://pypi.org/project/wwpdb.utils... 

Full wwPDB X-ray Structure Validation Report O i

otalT number of atoms 11450 wwPDB-VP verageA B, all atoms (Å 2) 23.0 wwPDB-VP Xtriage's analysis on translational NCS is as follows: The largest o -origin akep in the Patterson function is 4.91% of the height of the origin ak.ep No signi cant...

https://files.rcsb.org/pub/pdb/valid... 

wwPDB: X-Ray Validation

wwPDB: Worldwide Protein Data Bank. X-ray Validation Task Force. Method-specific Validation Task Forces have been convened to collect recommendations and develop consensus on additional validation that should be performed, and to identify software...

http://wwpdb-remediation.rutgers.edu... 

Outcome of the First wwPDB/CCDC/D3R Ligand Validation ...

Apr 05, 2016  · The wwPDB leadership in consultation with the wwPDB Advisory Committee will revisit this issue. Second, some participants strongly advocated mandatory PDB deposition of all-atom structural models, including computed ...

https://www.sciencedirect.com/scienc... 

Report of the wwPDB Small-Angle Scattering Task Force ...

Jun 04, 2013  · This report presents the conclusions of the July 12–13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, ...

https://www.cell.com/structure/fullt... 

Recommendations of the wwPDB NMR Validation Task Force.

Sep 03, 2013  · For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, stru...

https://www.ncbi.nlm.nih.gov/pubmed/... 

The Protein Data Bank at 40: Reflecting on the Past to ...

Mar 07, 2012  · The wwPDB now operates as a cohesive unit of equal partners to steward the world's structural data. wwPDB members collaborate on all issues related to the archive, including deposition and annotation policies, requir...

https://www.sciencedirect.com/scienc... 

GitHub - yokochi47/pdbx-validation: The pdbx-validation is ...

Mar 14, 2018  · pdbx-validation. The pdbx-validation is a generation tool of alternative wwPDB validation reports where validation metrics are reorganized using the familiar mmCIF naming scheme and categories. It includes PDBx/mmCIF...

https://github.com/yokochi47/pdbx-va... 

Data Item _struct_conn.pdbx_leaving_atom_flag

Item name _struct_conn.pdbx_leaving_atom_flag Category name struct_conn Attribute name pdbx_leaving_atom_flag Required in PDB entries no Used in current PDB entries

https://pdbml.wwpdb.org/dictionaries... 

RCSB PDB - 6Z5U: Cryo-EM structure of the A. baumannii ...

May 27, 2020  · As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches ba...

https://www1.rcsb.org/structure/6Z5U 

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