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1.
Nucleic Acids Res ; 51(D1): D488-D508, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36420884

RESUMO

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.


Assuntos
Inteligência Artificial , Bases de Dados de Proteínas , Proteínas , Aprendizado de Máquina , Conformação Proteica , Proteínas/química , Reprodutibilidade dos Testes
2.
Nucleic Acids Res ; 49(D1): D437-D451, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33211854

RESUMO

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Substâncias Macromoleculares/química , Conformação Proteica , Proteínas/química , Bioengenharia/métodos , Pesquisa Biomédica/métodos , Biotecnologia/métodos , COVID-19/epidemiologia , COVID-19/prevenção & controle , COVID-19/virologia , Humanos , Substâncias Macromoleculares/metabolismo , Pandemias , Proteínas/genética , Proteínas/metabolismo , SARS-CoV-2/genética , SARS-CoV-2/metabolismo , SARS-CoV-2/fisiologia , Software , Proteínas Virais/química , Proteínas Virais/genética , Proteínas Virais/metabolismo
3.
Nucleic Acids Res ; 47(D1): D464-D474, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30357411

RESUMO

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'


Assuntos
Bases de Dados de Proteínas , Conformação Proteica , Pesquisa Biomédica/educação , Biotecnologia/educação , Curadoria de Dados , Software
4.
Nucleic Acids Res ; 45(D1): D271-D281, 2017 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-27794042

RESUMO

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Proteínas/química , Proteínas/genética , Conjuntos de Dados como Assunto , Redes e Vias Metabólicas , Modelos Moleculares , Conformação Proteica , Proteínas/metabolismo , Software , Relação Estrutura-Atividade , Interface Usuário-Computador , Navegador
5.
Bioinformatics ; 33(13): 2047-2049, 2017 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-28334105

RESUMO

SUMMARY: We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures. We have integrated this package with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. By scanning all 3D structures in the PDB using BioJava-ModFinder, we identified more than 30 000 structures with protein modifications, which can be searched, browsed, and visualized on the RCSB PDB website. AVAILABILITY AND IMPLEMENTATION: BioJava-ModFinder is available as open source (LGPL license) at ( https://github.com/biojava/biojava/tree/master/biojava-modfinder ). The RCSB PDB can be accessed at http://www.rcsb.org . CONTACT: pwrose@ucsd.edu.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Conformação Proteica , Software , Internet
6.
Nucleic Acids Res ; 43(Database issue): D345-56, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25428375

RESUMO

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.


Assuntos
Bases de Dados de Proteínas , Conformação Proteica , Sítios de Ligação , Internet , Proteínas de Membrana/química , Biologia Molecular/educação , Anotação de Sequência Molecular , Complexos Multiproteicos/química , Peptídeos/química , Preparações Farmacêuticas/química , Pesquisa , Software
7.
Bioinformatics ; 31(1): 126-7, 2015 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-25183487

RESUMO

SUMMARY: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service. AVAILABILITY AND IMPLEMENTATION: RCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org).


Assuntos
Biologia Computacional/métodos , Gráficos por Computador , Bases de Dados de Proteínas , Aplicativos Móveis , Software , Pesquisa Biomédica , Humanos , Interface Usuário-Computador , Fluxo de Trabalho
8.
Nucleic Acids Res ; 41(Database issue): D475-82, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23193259

RESUMO

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.


Assuntos
Bases de Dados de Proteínas , Conformação Proteica , Bioquímica/educação , Gráficos por Computador , Internet , Ligantes , Estrutura Terciária de Proteína , Pesquisa , Homologia Estrutural de Proteína
9.
Nucleic Acids Res ; 39(Database issue): D392-401, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21036868

RESUMO

The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.


Assuntos
Bases de Dados de Proteínas , Proteínas/química , Animais , Gráficos por Computador , Humanos , Internet , Ligantes , Camundongos , Conformação Proteica , Integração de Sistemas , Interface Usuário-Computador
10.
Nucleic Acids Res ; 39(Database issue): D456-64, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-20935055

RESUMO

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global 'one-stop shop' resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.


Assuntos
Microscopia Crioeletrônica , Bases de Dados Factuais , Substâncias Macromoleculares/química , Proteínas/química , Bases de Dados de Proteínas , Substâncias Macromoleculares/ultraestrutura , Modelos Moleculares , Proteínas/ultraestrutura
11.
Front Bioinform ; 3: 1311287, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38111685

RESUMO

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

12.
J Mol Biol ; 435(14): 167994, 2023 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-36738985

RESUMO

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides open access to experimentally-determined three-dimensional (3D) structures of biomolecules. The RCSB PDB RCSB.org research-focused web portal is used annually by many millions of users around the world. They access biostructure information, run complex queries utilizing various search services (e.g., full-text, structural and chemical attribute, chemical, sequence, and structure similarity searches), and visualize macromolecules in 3D, all at no charge and with no limitations on data usage. Notwithstanding more than 24,000-fold growth of the PDB over the past five decades, experimentally-determined structures are only available for a small subset of the millions of proteins of known sequence. Recently developed machine learning software tools can predict 3D structures of proteins at accuracies comparable to lower-resolution experimental methods. The RCSB PDB now provides access to ∼1,000,000 Computed Structure Models (CSMs) of proteins coming from AlphaFold DB and the ModelArchive alongside ∼200,000 experimentally-determined PDB structures. Both CSMs and PDB structures are available on RCSB.org and via well-established RCSB PDB Data, Search, and 1D-Coordinates application programming interfaces (APIs). Simultaneous delivery of PDB data and CSMs provides users with access to complementary structural information across the human proteome and those of model organisms and selected pathogens. API enhancements are backwards-compatible and programmatic users can "opt in" to access CSMs with minimal effort. Herein, we describe modifications to RCSB PDB cyberinfrastructure required to support sixfold scaling of 3D biostructure data delivery and lay the groundwork for scaling to accommodate hundreds of millions of CSMs.


Assuntos
Biologia Computacional , Bases de Dados de Proteínas , Humanos , Biologia Computacional/métodos , Conformação Proteica , Proteoma , Software
13.
Protein Sci ; 31(1): 187-208, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34676613

RESUMO

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.


Assuntos
Biologia Computacional/história , Bases de Dados de Proteínas/história , Interface Usuário-Computador , Aniversários e Eventos Especiais , História do Século XX , História do Século XXI
14.
Protein Sci ; 31(12): e4482, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36281733

RESUMO

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.


Assuntos
Biologia Computacional , Proteínas , Humanos , Conformação Proteica , Bases de Dados de Proteínas , Proteínas/química , Biologia Computacional/métodos , Substâncias Macromoleculares/química
15.
J Mol Biol ; 433(11): 166704, 2021 05 28.
Artigo em Inglês | MEDLINE | ID: mdl-33186584

RESUMO

The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique users worldwide by delivering experimentally-determined 3D structures of biomolecules integrated with >40 external data resources via RCSB.org, application programming interfaces (APIs), and FTP downloads. Herein, we present the architectural redesign of RCSB PDB data delivery services that build on existing PDBx/mmCIF data schemas. New data access APIs (data.rcsb.org) enable efficient delivery of all PDB archive data. A novel GraphQL-based API provides flexible, declarative data retrieval along with a simple-to-use REST API. A powerful new search system (search.rcsb.org) seamlessly integrates heterogeneous types of searches across the PDB archive. Searches may combine text attributes, protein or nucleic acid sequences, small-molecule chemical descriptors, 3D macromolecular shapes, and sequence motifs. The new RCSB.org architecture adheres to the FAIR Principles, empowering users to address a wide array of research problems in fundamental biology, biomedicine, biotechnology, bioengineering, and bioenergy.


Assuntos
Biologia Computacional , Bases de Dados de Proteínas , Substâncias Macromoleculares/química , Ferramenta de Busca
16.
J Agric Food Chem ; 65(47): 10206-10213, 2017 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-29112818

RESUMO

A study was performed to identify metabolic processes associated with ß-ODAP synthesis in grass pea using a metabolomics approach. GC-MS metabolomics was performed on seedlings at 2, 6, and 25 days after sowing. A total of 141 metabolites were detected among the three time points representing much of grass pea primary metabolism, including amino acids, carbohydrates, purines, and others. Principal component analysis revealed unique metabolite profiles of grass pea tissues among the three time points. Fold change, hierarchical clustering, and orthogonal projections to latent structures-discriminant analyses, and biochemical pathway ontologies were used to characterize covariance of metabolites with ß-ODAP content. The data indicates that alanine and nitrogen metabolism, cysteine and sulfur metabolism, and purine, pyrimidine, and pyridine metabolism were associated with ß-ODAP metabolism. Our results reveal the metabolite profiles in grass pea development and provide insights into mechanisms of ß-ODAP accumulation and degradation.


Assuntos
Diamino Aminoácidos/biossíntese , Lathyrus/metabolismo , Aminoácidos/análise , Aminoácidos/metabolismo , Cromatografia Gasosa-Espectrometria de Massas , Lathyrus/química , Lathyrus/crescimento & desenvolvimento , Metabolômica , Plântula/química , Plântula/crescimento & desenvolvimento , Plântula/metabolismo
18.
Database (Oxford) ; 2011: bar003, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21382834

RESUMO

The RCSB Protein Data Bank (RCSB PDB, www.pdb.org) is a key online resource for structural biology and related scientific disciplines. The website is used on average by 165,000 unique visitors per month, and more than 2000 other websites link to it. The amount and complexity of PDB data as well as the expectations on its usage are growing rapidly. Therefore, ensuring the reliability and robustness of the RCSB PDB query and distribution systems are crucially important and increasingly challenging. This article describes quality assurance for the RCSB PDB website at several distinct levels, including: (i) hardware redundancy and failover, (ii) testing protocols for weekly database updates, (iii) testing and release procedures for major software updates and (iv) miscellaneous monitoring and troubleshooting tools and practices. As such it provides suggestions for how other websites might be operated.


Assuntos
Bases de Dados de Proteínas/normas , Internet/normas , Computadores , Controle de Qualidade , Software , Interface Usuário-Computador
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