Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 56
Filtrar
1.
J Mol Biol ; : 168546, 2024 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-38508301

RESUMEN

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.

2.
Structure ; 2024 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-38490206

RESUMEN

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NEF and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB restraint violation report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.

3.
bioRxiv ; 2024 Jan 22.
Artículo en Inglés | MEDLINE | ID: mdl-38328042

RESUMEN

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB Restraint Violation Report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.

4.
IUCrJ ; 11(Pt 2): 140-151, 2024 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-38358351

RESUMEN

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.


Asunto(s)
Curaduría de Datos , Microscopía por Crioelectrón/métodos
5.
ArXiv ; 2024 Feb 02.
Artículo en Inglés | MEDLINE | ID: mdl-38076521

RESUMEN

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

6.
J Mol Biol ; 435(14): 167994, 2023 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-36738985

RESUMEN

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.


Asunto(s)
Biología Computacional , Bases de Datos de Proteínas , Humanos , Biología Computacional/métodos , Conformación Proteica , Proteoma , Programas Informáticos
7.
J Mol Biol ; 435(14): 168021, 2023 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-36828268

RESUMEN

ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.


Asunto(s)
Bases de Datos de Proteínas , Sustancias Macromoleculares/química , Conformación Proteica , Programas Informáticos
8.
Nucleic Acids Res ; 51(D1): D488-D508, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36420884

RESUMEN

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.


Asunto(s)
Inteligencia Artificial , Bases de Datos de Proteínas , Proteínas , Aprendizaje Automático , Conformación Proteica , Proteínas/química , Reproducibilidad de los Resultados
9.
Biophys Rev ; 14(6): 1281-1301, 2022 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-36474933

RESUMEN

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

10.
Biomolecules ; 12(10)2022 10 04.
Artículo en Inglés | MEDLINE | ID: mdl-36291635

RESUMEN

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.


Asunto(s)
Biología Computacional , Proteínas , Humanos , Conformación Proteica , Bases de Datos de Proteínas , Biología Computacional/métodos , Proteínas/química , Estudiantes
11.
Protein Sci ; 31(12): e4482, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36281733

RESUMEN

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.


Asunto(s)
Biología Computacional , Proteínas , Humanos , Conformación Proteica , Bases de Datos de Proteínas , Proteínas/química , Biología Computacional/métodos , Sustancias Macromoleculares/química
12.
J Mol Biol ; 434(11): 167599, 2022 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-35460671

RESUMEN

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.


Asunto(s)
Biología Computacional , Cristalografía , Bases de Datos de Proteínas , Programas Informáticos , Sustancias Macromoleculares/química , Biología Molecular , Conformación Proteica , Semántica
13.
Structure ; 30(2): 252-262.e4, 2022 02 03.
Artículo en Inglés | MEDLINE | ID: mdl-35026162

RESUMEN

More than 70% of the experimentally determined macromolecular structures in the Protein Data Bank (PDB) contain small-molecule ligands. Quality indicators of ∼643,000 ligands present in ∼106,000 PDB X-ray crystal structures have been analyzed. Ligand quality varies greatly with regard to goodness of fit between ligand structure and experimental data, deviations in bond lengths and angles from known chemical structures, and inappropriate interatomic clashes between the ligand and its surroundings. Based on principal component analysis, correlated quality indicators of ligand structure have been aggregated into two largely orthogonal composite indicators measuring goodness of fit to experimental data and deviation from ideal chemical structure. Ranking of the composite quality indicators across the PDB archive enabled construction of uniformly distributed composite ranking score. This score is implemented at RCSB.org to compare chemically identical ligands in distinct PDB structures with easy-to-interpret two-dimensional ligand quality plots, allowing PDB users to quickly assess ligand structure quality and select the best exemplars.


Asunto(s)
Proteínas/química , Proteínas/metabolismo , Bibliotecas de Moléculas Pequeñas/farmacología , Bases de Datos de Proteínas , Ligandos , Modelos Moleculares , Conformación Proteica
14.
Protein Sci ; 31(1): 187-208, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34676613

RESUMEN

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.


Asunto(s)
Biología Computacional/historia , Bases de Datos de Proteínas/historia , Interfaz Usuario-Computador , Aniversarios y Eventos Especiales , Historia del Siglo XX , Historia del Siglo XXI
15.
Proteins ; 90(5): 1054-1080, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-34580920

RESUMEN

Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.


Asunto(s)
COVID-19 , Pandemias , Aminoácidos , Humanos , Estudios Prospectivos , Proteoma , SARS-CoV-2 , Proteínas Virales/genética , Proteínas Virales/metabolismo
16.
Bioinformatics ; 38(5): 1452-1454, 2022 02 07.
Artículo en Inglés | MEDLINE | ID: mdl-34864908

RESUMEN

MOTIVATION: Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. RESULTS: We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. AVAILABILITY AND IMPLEMENTATION: Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Proteínas de la Membrana , Programas Informáticos , Humanos , Conformación Proteica , Bases de Datos de Proteínas , Secuencia de Aminoácidos
17.
Acta Crystallogr D Struct Biol ; 77(Pt 12): 1486-1496, 2021 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-34866606

RESUMEN

Structures of many complex biological assemblies are increasingly determined using integrative approaches, in which data from multiple experimental methods are combined. A standalone system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. Here, the data standards and software tools that support PDB-Dev are described along with the new and updated components of the PDB-Dev data-collection, processing and archiving infrastructure. Following the FAIR (Findable, Accessible, Interoperable and Reusable) principles, PDB-Dev ensures that the results of integrative structure determinations are freely accessible to everyone.


Asunto(s)
Bases de Datos de Proteínas , Almacenamiento y Recuperación de la Información/métodos , Conformación Proteica , Proteínas/química
18.
Glycobiology ; 31(9): 1204-1218, 2021 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-33978738

RESUMEN

Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.


Asunto(s)
Carbohidratos , Proteínas , Carbohidratos/química , Bases de Datos de Proteínas , Proteínas/química
19.
Structure ; 29(4): 393-400.e1, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-33657417

RESUMEN

The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery.


Asunto(s)
Carbohidratos/química , Bases de Datos de Proteínas/normas , Simulación del Acoplamiento Molecular/métodos , Proteómica/métodos , Bibliotecas de Moléculas Pequeñas/química , Quimioinformática/métodos , Bases de Datos de Compuestos Químicos/normas , Humanos , Ligandos , Unión Proteica , Proteoma/química , Proteoma/metabolismo
20.
Campbell Syst Rev ; 17(3): e1185, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37052419

RESUMEN

Background: The incidence of autism spectrum disorders (ASD) is on the rise. Currently, 1 in 59 children are identified with ASD in the United States. ASD refers to a range of neurological disorders that involve some degree of difficulty with communication and interpersonal relationships. The range of the spectrum for autism disorders is wide with those at the higher functioning end often able to lead relatively independent lives and complete academic programs even while demonstrating social awkwardness. Those at the lower functioning end of the autism spectrum often demonstrate physical limitations, may lack speech, and have the inability to relate socially with others. As persons with ASD age, options such as employment become increasingly important as a consideration for long-term personal planning and quality of life. While many challenges exist for persons with ASD in obtaining and maintaining employment, some research shows that, with effective behavioral and social interventions, employment can occur. About 37% of individuals with ASD report having been employed for 12 months or more, 4 years after exiting high school. However, several studies show that individuals with ASD are more likely to lose their employment for behavioral and social interaction problems rather than their inability to perform assigned work tasks. Although Westbrook et al. (2012a, 2013, 2015) have reviewed the literature on interventions targeting employment for individuals with ASD, this review is outdated and does not account for recent developments in the field. Objectives: The objective of this review is to determine the effectiveness of employment interventions in securing and maintaining employment for adults and transition-age youth with ASD, updating two reviews by Westbrook et al. (2012a, 2013). Search Methods: The comprehensive search strategy used to identify relevant studies included a review of 28 relevant electronic databases. Search terminology for each of the electronic databases was developed from available database thesauri. Appropriate synonyms were used to maximize the database search output. Several international databases were included among the 28 databases searched. In addition, the authors identified and reviewed gray literature through analysis of reference lists of relevant studies. Unpublished dissertations and theses were also identified through database searches. The programs of conferences held by associations and organizations relevant to ASD and employment were also searched. In sum, the search strategy replicated and expanded the prior search methods used by Westbrook et al. (2012a, 2013). Selection Criteria: Selection criteria consisted of an intervention evaluation using a randomized controlled trial or quasi-experimental design, an employment outcome, and a population of individuals with ASD. Data Collection and Analysis: We updated the search from Westbrook et al., replicating and broadening the information retrieval processes. Our wide array of sources included electronic databases, gray literature, and conference and organization websites. Once all potentially relevant studies were located, pairs of coders evaluated the relevance of each title and abstract. Among the studies deemed potentially relevant, 278 were subjected to full-text retrieval and screening by pairs of coders. Because many intervention studies did not include employment outcomes, only three studies met our inclusion criteria. Given the small number of included studies, meta-analytic procedures were not used; rather, we opted to use more narrative and descriptive analysis to summarize the available evidence, including an assessment of risk of bias. Results: The systematic review update identified three studies that evaluated employment outcomes for interventions for individuals with ASD. All three studies identified in the review suggest that vocation-focused programs may have positive impacts on the employment outcomes for individuals with ASD. Wehman et al. indicated that participants in Project SEARCH had higher employment rates than control participants at both 9-month and 1-year follow-up time points. Adding autism spectrum disorder supports, Project SEARCH in Wehman et al.'s study also demonstrated higher employment rates for treatment participants than control participants at postgraduation, 3-month follow-up, and 12-month follow-up. Smith et al. found that virtual reality job interview training was able to increase the number of job offers treatment participants received compared to control participants. Authors' Conclusions: Given that prior reviews did not identify interventions with actual employment outcomes, the more recent emergence of evaluations of such programs is encouraging. This suggests that there is a growing body of evidence regarding interventions to enhance the employment outcomes for individuals with ASD but also greater need to conduct rigorous trials of vocation-based interventions for individuals with ASD that measure employment outcomes.

SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA
...