Journal of Molecular Biology最新文献_第10页

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods IHMCIF：整合结构确定方法的 PDBx/mmCIF 数据标准扩展。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168546

{"title":"IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods","authors":"","doi":"10.1016/j.jmb.2024.168546","DOIUrl":"10.1016/j.jmb.2024.168546","url":null,"abstract":"<div><p>IHMCIF (<span><span>github.com/ihmwg/IHMCIF</span><svg><path></path></svg></span>) 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 (<em>FAIR</em>). 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 (<span><span>wwpdb.org/task/hybrid</span><svg><path></path></svg></span>). 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.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168546"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624001414/pdfft?md5=7a3e7aade30878dc264a3e57ea5efe5f&pid=1-s2.0-S0022283624001414-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140178792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research 叶片衰老数据库 v5.0：促进植物衰老研究的综合资料库。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168530

{"title":"Leaf Senescence Database v5.0: A Comprehensive Repository for Facilitating Plant Senescence Research","authors":"","doi":"10.1016/j.jmb.2024.168530","DOIUrl":"10.1016/j.jmb.2024.168530","url":null,"abstract":"<div><p>Through an extensive literature survey, we have upgraded the Leaf Senescence Database (LSD v5.0; <span><span>https://ngdc.cncb.ac.cn/lsd/</span><svg><path></path></svg></span>), a curated repository of comprehensive senescence-associated genes (SAGs) and their corresponding mutants. Since its inception in 2010, LSD undergoes frequent updates to encompass the latest advances in leaf senescence research and its current version comprises a high-quality collection of 31,740 SAGs and 1,209 mutants from 148 species, which were manually searched based on robust experimental evidence and further categorized according to their functions in leaf senescence. Furthermore, LSD was greatly enriched with comprehensive annotations for the SAGs through meticulous curation using both manual and computational methods. In addition, it was equipped with user-friendly web interfaces that facilitate text queries, BLAST searches, and convenient download of SAG sequences for localized analysis. Users can effortlessly navigate the database to access a plethora of information, including literature references, mutants, phenotypes, multi-omics data, miRNA interactions, homologs in other plants, and cross-links to various databases. Taken together, the upgraded version of LSD stands as the most comprehensive and informative plant senescence-related database to date, incorporating the largest collection of SAGs and thus bearing great utility for a wide range of studies related to plant senescence.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168530"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624001177/pdfft?md5=4966a0c80ee9743534f4c43a1fe22860&pid=1-s2.0-S0022283624001177-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140093171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alpha&ESMhFolds: A Web Server for Comparing AlphaFold2 and ESMFold Models of the Human Reference Proteome Alpha&ESMhFolds：用于比较人类参考蛋白质组的 AlphaFold2 和 ESMFold 模型的网络服务器。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168593

引用次数: 0

TPPU_DSF: A Web Application to Calculate Thermodynamic Parameters Using DSF Data TPPU_DSF：利用 DSF 数据计算热力学参数的网络应用程序

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168519

{"title":"TPPU_DSF: A Web Application to Calculate Thermodynamic Parameters Using DSF Data","authors":"","doi":"10.1016/j.jmb.2024.168519","DOIUrl":"10.1016/j.jmb.2024.168519","url":null,"abstract":"<div><p>Here we present TPPU_DSF (<span><span>https://maciasnmr.net/tppu_dsf/</span><svg><path></path></svg></span>). This is a free and open-source web application that opens, converts, fits, and calculates the thermodynamic parameters of protein unfolding from standard differential scanning fluorimetry (DSF) data in an automated manner. The software has several applications. In the context of screening compound libraries for protein binders, obtaining thermodynamic parameters provides a more robust approach to detecting hits than the changes in the melting temperature (T<sub>m</sub>) alone, thereby helping to increase the number of positive hits in screening campaigns. Moreover, changes in ΔG<sub>u</sub><sup>o</sup> indicate protein response to binding at lower compound concentrations than those in the T<sub>m</sub>, thereby reducing the costs associated with the amounts of protein and compounds required for the assays. Also, by adding thermodynamic information to the T<sub>m</sub> comparison, the software can contribute to the optimization of protein constructs and buffer conditions, a common practice before structural and functional projects.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168519"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624001062/pdfft?md5=cf58214544ee4ccc6fb33b70056879e3&pid=1-s2.0-S0022283624001062-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140099308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational Resources for Molecular Biology 2024 分子生物学计算资源 2024。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168739

Rita Casadio, David H. Mathews, Michael J.E. Sternberg

引用次数: 0

MVAR: A Mouse Variation Registry MVAR：小鼠变异登记册。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168518

{"title":"MVAR: A Mouse Variation Registry","authors":"","doi":"10.1016/j.jmb.2024.168518","DOIUrl":"10.1016/j.jmb.2024.168518","url":null,"abstract":"<div><p>The Mouse Variation Registry (MVAR) resource is a scalable registry of mouse single nucleotide variants and small indels and variant annotation. The resource accepts data in standard Variant Call Format (VCF) and assesses the uniqueness of the submitted variants via a canonicalization process. Novel variants are assigned a unique, persistent MVAR identifier; variants that are equivalent to an existing variant in the resource are associated with the existing identifier. Annotations for variant type, molecular consequence, impact, and genomic region in the context of specific transcripts and protein sequences are generated using Ensembl’s Variant Effect Predictor (VEP) and Jannovar. Access to the data and annotations in MVAR are supported via an Application Programming Interface (API) and web application. Researchers can search the resource by gene symbol, genomic region, variant (expressed in Human Genome Variation Society syntax), refSNP identifiers, or MVAR identifiers. Tabular search results can be filtered by variant annotations (variant type, molecular consequence, impact, variant region) and viewed according to variant distribution across mouse strains. The registry currently comprises more than 99 million canonical single nucleotide variants for 581 strains of mice. MVAR is accessible from <span><span>https://mvar.jax.org</span><svg><path></path></svg></span>.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168518"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624001050/pdfft?md5=6a3249ee01b7788a6e26ba3e34d23bf6&pid=1-s2.0-S0022283624001050-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140064505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DockThor-VS: A Free Platform for Receptor-Ligand Virtual Screening DockThor-VS：受体配体虚拟筛选的免费平台

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168548

{"title":"DockThor-VS: A Free Platform for Receptor-Ligand Virtual Screening","authors":"","doi":"10.1016/j.jmb.2024.168548","DOIUrl":"10.1016/j.jmb.2024.168548","url":null,"abstract":"<div><p>The DockThor-VS platform (<span><span>https://dockthor.lncc.br/v2/</span><svg><path></path></svg></span>) is a free protein–ligand docking server conceptualized to facilitate and assist drug discovery projects to perform docking-based virtual screening experiments accurately and using high-performance computing. The DockThor docking engine is a grid-based method designed for flexible-ligand and rigid-receptor docking. It employs a multiple-solution genetic algorithm and the MMFF94S molecular force field scoring function for pose prediction. This engine was engineered to handle highly flexible ligands, such as peptides. Affinity prediction and ranking of protein–ligand complexes are performed with the linear empirical scoring function DockTScore. The main steps of the ligand and protein preparation are available on the DockThor Portal, making it possible to change the protonation states of the amino acid residues, and include cofactors as rigid entities. The user can also customize and visualize the main parameters of the grid box. The results of docking experiments are automatically clustered and ordered, providing users with a diverse array of meaningful binding modes. The platform DockThor-VS offers a user-friendly interface and powerful algorithms, enabling researchers to conduct virtual screening experiments efficiently and accurately. The DockThor Portal utilizes the computational strength of the Brazilian high-performance platform SDumont, further amplifying the efficiency and speed of docking experiments. Additionally, the web server facilitates and enhances virtual screening experiments by offering curated structures of potential targets and compound datasets, such as proteins related to COVID-19 and FDA-approved drugs for repurposing studies. In summary, DockThor-VS is a dynamic and evolving solution for docking-based virtual screening to be applied in drug discovery projects.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168548"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624001438/pdfft?md5=57349e8fba1907bce8b7894215619c89&pid=1-s2.0-S0022283624001438-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140282959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles EVPsort：细胞外囊泡和颗粒中的小 ncRNA 图谱和分选图谱

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168571

{"title":"EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles","authors":"","doi":"10.1016/j.jmb.2024.168571","DOIUrl":"10.1016/j.jmb.2024.168571","url":null,"abstract":"<div><p>Extracellular vesicles and particles (EVPs) play a crucial role in mediating cell-to-cell communication by transporting various molecular cargos, with small non-coding RNAs (ncRNAs) holding particular significance. A thorough investigation into the abundance and sorting mechanisms of ncRNA within EVPs is imperative for advancing their clinical applications. We have developed EVPsort, which not only provides an extensive overview of ncRNA profiling in 3,162 samples across various biofluids, cell lines, and disease contexts but also seamlessly integrates 19 external databases and tools. This integration encompasses information on associations between ncRNAs and RNA-binding proteins (RBPs), motifs, targets, pathways, diseases, and drugs. With its rich resources and powerful analysis tools, EVPsort extends its profiling capabilities to investigate ncRNA sorting, identify relevant RBPs and motifs, and assess functional implications. EVPsort stands as a pioneering database dedicated to comprehensively addressing both the abundance and sorting of ncRNA within EVPs. It is freely accessible at <span><span>https://bioinfo.vanderbilt.edu/evpsort/</span><svg><path></path></svg></span>.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168571"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624001669/pdfft?md5=d1e4fae061b08442f9953654a1bc6eaa&pid=1-s2.0-S0022283624001669-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140591914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

@TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking @TOME 3.0：蛋白质结构建模与配体对接的接口

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168704

Jean-Luc Pons , Victor Reys , François Grand , Violaine Moreau , Jerôme Gracy , Thomas E. Exner , Gilles Labesse

{"title":"@TOME 3.0: Interfacing Protein Structure Modeling and Ligand Docking","authors":"Jean-Luc Pons , Victor Reys , François Grand , Violaine Moreau , Jerôme Gracy , Thomas E. Exner , Gilles Labesse","doi":"10.1016/j.jmb.2024.168704","DOIUrl":"10.1016/j.jmb.2024.168704","url":null,"abstract":"<div><p>Knowledge of protein–ligand complexes is essential for efficient drug design. Virtual docking can bring important information on putative complexes but it is still far from being simultaneously fast and accurate. Receptors are flexible and adapt to the incoming small molecules while docking is highly sensitive to small conformational deviations. Conformation ensemble is providing a mean to simulate protein flexibility. However, modeling multiple protein structures for many targets is seldom connected to ligand screening in an efficient and straightforward manner.</p><p>@TOME-3 is an updated version of our former pipeline @TOME-2, in which protein structure modeling is now directly interfaced with flexible ligand docking. Sequence-sequence profile comparisons identify suitable PDB templates for structure modeling and ligands from these templates are used to deduce binding sites to be screened. In addition, bound ligand can be used as pharmacophoric restraint during the virtual docking. The latter is performed by PLANTS while the docking poses are analysed through multiple chemoinformatics functions. This unique combination of tools allows rapid and efficient ligand docking on multiple receptor conformations in parallel. @TOME-3 is freely available on the web at <span><span>https://atome.cbs.cnrs.fr</span><svg><path></path></svg></span>.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168704"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624003139/pdfft?md5=88c6a60894400d42c3d2f8977cdcdff1&pid=1-s2.0-S0022283624003139-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141713094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AHoJ-DB: A PDB-wide Assignment of apo & holo Relationships Based on Individual Protein–Ligand Interactions AHoJ-DB：基于单个蛋白质与配体的相互作用，在整个 PDB 范围内分配 apo 和 holo 关系。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168545

{"title":"AHoJ-DB: A PDB-wide Assignment of apo & holo Relationships Based on Individual Protein–Ligand Interactions","authors":"","doi":"10.1016/j.jmb.2024.168545","DOIUrl":"10.1016/j.jmb.2024.168545","url":null,"abstract":"<div><p>A single protein structure is rarely sufficient to capture the conformational variability of a protein. Both bound and unbound (holo and apo) forms of a protein are essential for understanding its geometry and making meaningful comparisons. Nevertheless, docking or drug design studies often still consider only single protein structures in their holo form, which are for the most part rigid. With the recent explosion in the field of structural biology, large, curated datasets are urgently needed. Here, we use a previously developed application (AHoJ) to perform a comprehensive search for apo-holo pairs for 468,293 biologically relevant protein–ligand interactions across 27,983 proteins. In each search, the binding pocket is captured and mapped across existing structures within the same UniProt, and the mapped pockets are annotated as apo or holo, based on the presence or absence of ligands. We assemble the results into a database, AHoJ-DB (<span><span>www.apoholo.cz/db</span><svg><path></path></svg></span>), that captures the variability of proteins with identical sequences, thereby exposing the agents responsible for the observed differences in geometry. We report several metrics for each annotated pocket, and we also include binding pockets that form at the interface of multiple chains. Analysis of the database shows that about 24% of the binding sites occur at the interface of two or more chains and that less than 50% of the total binding sites processed have an apo form in the PDB. These results can be used to train and evaluate predictors, discover potentially druggable proteins, and reveal protein- and ligand-specific relationships that were previously obscured by intermittent or partial data.</p><p>Availability: <span><span>www.apoholo.cz/db</span><svg><path></path></svg></span></p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168545"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624001402/pdfft?md5=f8fea6cdc88d1aafc3fe11d1d30c7887&pid=1-s2.0-S0022283624001402-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140178790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0