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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 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168571

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 https://bioinfo.vanderbilt.edu/evpsort/.

细胞外囊泡和颗粒(EVPs)通过运输各种分子载体,在介导细胞间通讯方面发挥着至关重要的作用,其中小的非编码 RNA(ncRNA)尤为重要。深入研究 EVP 中 ncRNA 的丰度和分拣机制对于推动其临床应用至关重要。我们开发了 EVPsort,它不仅提供了 3162 份样本中各种生物流体、细胞系和疾病背景下 ncRNA 图谱的广泛概述,还无缝整合了 19 个外部数据库和工具。这种整合涵盖了 ncRNA 与 RNA 结合蛋白 (RBP)、主题、靶点、通路、疾病和药物之间的关联信息。凭借丰富的资源和强大的分析工具,EVPsort 扩展了其剖析功能,以研究 ncRNA 排序、识别相关 RBPs 和基调并评估功能影响。EVPsort 是一个开创性的数据库,致力于全面研究 EVPs 中 ncRNA 的丰度和排序。该数据库可通过以下网址免费访问:.
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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 Q1 BIOCHEMISTRY & 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

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.

@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 https://atome.cbs.cnrs.fr.

了解蛋白质配体复合物对于高效药物设计至关重要。虚拟对接可以为假定的复合物提供重要信息,但它还远远不能同时做到快速和准确。受体是灵活的,能适应进入的小分子,而对接对微小的构象偏差非常敏感。构象组合为模拟蛋白质的灵活性提供了一种方法。@TOME-3是我们以前管道@TOME-2的升级版本,其中蛋白质结构建模现在直接与灵活配体对接相连接。序列-序列剖面比较可以为结构建模确定合适的 PDB 模板,而这些模板中的配体则用于推导待筛选的结合位点。此外,结合配体还可在虚拟对接过程中用作药效抑制剂。后者由 PLANTS 完成,同时通过多种化学信息学功能对对接姿势进行分析。这种独特的工具组合可以并行地对多个受体构象进行快速高效的配体对接。@TOME-3 可在 https://atome.cbs.cnrs.fr 网站上免费获取。
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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 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168545

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 (www.apoholo.cz/db), 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.

Availability: www.apoholo.cz/db

单一的蛋白质结构很少足以捕捉到蛋白质的构象变化。要了解蛋白质的几何结构并进行有意义的比较,蛋白质的结合型和非结合型(整体型和非整体型)都是必不可少的。然而,对接或药物设计研究通常仍然只考虑整体形式的单一蛋白质结构,这种结构大多是刚性的。随着最近结构生物学领域的爆炸式发展,迫切需要大型的、经过整理的数据集。在这里,我们使用以前开发的应用程序(AHoJ)对 27983 个蛋白质中 468293 个与生物学相关的蛋白质-配体相互作用的 apo-holo 对进行了全面搜索。在每次搜索中,我们都会捕捉结合口袋,并将其映射到同一 UniProt 中的现有结构中,然后根据配体的存在或不存在,将映射口袋标注为 apo 或 holo。我们将结果汇总到一个数据库 AHoJ-DB (www.apoholo.cz/db),该数据库捕捉了具有相同序列的蛋白质的变异性,从而揭示了造成所观察到的几何差异的原因。我们报告了每个注释口袋的若干指标,还包括在多链界面形成的结合口袋。对数据库的分析表明,约 24% 的结合位点出现在两条或两条以上链的界面上,而在 PDB 中处理过的总结合位点中,有 apo 形式的不到 50%。这些结果可用于训练和评估预测因子,发现潜在的可药用蛋白质,并揭示蛋白质和配体之间的特异性关系,而这些关系以前因数据断断续续或部分数据而模糊不清。可用性:http://apoholo.cz/db。
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引用次数: 0
BeetleAtlas: An Ontogenetic and Tissue-specific Transcriptomic Atlas of the Red Flour Beetle Tribolium castaneum 甲虫图谱:红面粉甲虫(Tribolium castaneum)的个体发育和组织特异性转录组图集
IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168520

The red flour beetle Tribolium castaneum has emerged as a powerful model in insect functional genomics. However, a major limitation in the field is the lack of a detailed spatio-temporal view of the genetic signatures underpinning the function of distinct tissues and life stages. Here, we present an ontogenetic and tissue-specific web-based resource for Tribolium transcriptomics: BeetleAtlas (https://www.beetleatlas.org). This web application provides access to a database populated with quantitative expression data for nine adult and seven larval tissues, as well as for four embryonic stages of Tribolium. BeetleAtlas allows one to search for individual Tribolium genes to obtain values of both total gene expression and enrichment in different tissues, together with data for individual isoforms. To facilitate cross-species studies, one can also use Drosophila melanogaster gene identifiers to search for related Tribolium genes. For retrieved genes there are options to identify and display the tissue expression of related Tribolium genes or homologous Drosophila genes. Five additional search modes are available to find genes conforming to any of the following criteria: exhibiting high expression in a particular tissue; showing significant differences in expression between larva and adult; having a peak of expression at a specific stage of embryonic development; belonging to a particular functional category; and displaying a pattern of tissue expression similar to that of a query gene. We illustrate how the different feaures of BeetleAtlas can be used to illuminate our understanding of the genetic mechanisms underpinning the biology of what is the largest animal group on earth.

红粉甲虫(Tribolium castaneum)已成为昆虫功能基因组学的强大模型。然而,该领域的一个主要局限是缺乏对不同组织和生命阶段功能的遗传特征的详细时空观。在这里,我们介绍了一种基于本体和组织特异性的 Tribolium 转录组学网络资源:BeetleAtlas (https://www.beetleatlas.org)。该网络应用程序提供了一个数据库,其中包含蒺藜九个成体和七个幼体组织以及四个胚胎阶段的定量表达数据。BeetleAtlas 允许搜索单个蒺藜基因,以获得不同组织中的总基因表达值和富集度,以及单个同工酶的数据。为便于跨物种研究,还可以使用黑腹果蝇基因标识符搜索相关的蒺藜基因。对于检索到的基因,可选择识别和显示相关铁蒺藜基因或同源果蝇基因的组织表达。另外还有五种搜索模式可用于查找符合以下任何标准的基因:在特定组织中表现出高表达;在幼虫和成虫之间表现出显著的表达差异;在胚胎发育的特定阶段达到表达峰值;属于特定的功能类别;表现出与查询基因相似的组织表达模式。我们将说明如何利用 BeetleAtlas 的不同功能来阐明我们对地球上最大动物群体生物学遗传机制的理解。
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引用次数: 0
LinearAlifold: Linear-time consensus structure prediction for RNA alignments LinearAlifold:RNA 对齐的线性时间共识结构预测
IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168694

Predicting the consensus structure of a set of aligned RNA homologs is a convenient method to find conserved structures in an RNA genome, which has many applications including viral diagnostics and therapeutics. However, the most commonly used tool for this task, RNAalifold, is prohibitively slow for long sequences, due to a cubic scaling with the sequence length, taking over a day on 400 SARS-CoV-2 and SARS-related genomes (30,000nt). We present LinearAlifold, a much faster alternative that scales linearly with both the sequence length and the number of sequences, based on our work LinearFold that folds a single RNA in linear time. Our work is orders of magnitude faster than RNAalifold (0.7 h on the above 400 genomes, or 36× speedup) and achieves higher accuracies when compared to a database of known structures. More interestingly, LinearAlifold’s prediction on SARS-CoV-2 correlates well with experimentally determined structures, substantially outperforming RNAalifold. Finally, LinearAlifold supports two energy models (Vienna and BL*) and four modes: minimum free energy (MFE), maximum expected accuracy (MEA), ThreshKnot, and stochastic sampling, each of which takes under an hour for hundreds of SARS-CoV variants. Our resource is at:

https://github.com/LinearFold/LinearAlifold (code) and http://linearfold.org/linear-alifold (server).

预测一组对齐的 RNA 同源物的共识结构是发现 RNA 基因组中保守结构的一种便捷方法,它在病毒诊断和治疗等方面有很多应用。然而,最常用的工具 RNAalifold 在处理长序列时,由于序列长度呈立方缩放,速度慢得令人望而却步,处理 400 个 SARS-CoV-2 和 SARS 相关基因组(∼30,000nt)需要花费一天多的时间。我们提出的 LinearAlifold 是一种更快的替代方法,它与序列长度和序列数量成线性比例,以我们在线性时间内折叠单个 RNA 的工作 LinearFold 为基础。我们的工作比 RNAalifold 快几个数量级(在上述 400 个基因组上只需 0.7 个小时,即速度提高了 36 倍),而且与已知结构数据库相比,精度更高。更有趣的是,LinearAlifold 对 SARS-CoV-2 的预测与实验确定的结构有很好的相关性,大大超过了 RNAalifold。最后,LinearAlifold 支持两种能量模型(Vienna 和 BL*)和四种模式:最小自由能 (MFE)、最大预期准确度 (MEA)、ThreshKnot 和随机抽样,其中每种模式对数百种 SARS-CoV 变体的预测时间都在一小时以内。我们的资源位于:https://github.com/LinearFold/LinearAlifold(代码)和 http://linearfold.org/linear-alifold(服务器)。
{"title":"LinearAlifold: Linear-time consensus structure prediction for RNA alignments","authors":"","doi":"10.1016/j.jmb.2024.168694","DOIUrl":"10.1016/j.jmb.2024.168694","url":null,"abstract":"<div><p>Predicting the consensus structure of a set of aligned RNA homologs is a convenient method to find conserved structures in an RNA genome, which has many applications including viral diagnostics and therapeutics. However, the most commonly used tool for this task, RNAalifold, is prohibitively slow for long sequences, due to a cubic scaling with the sequence length, taking over a day on 400 SARS-CoV-2 and SARS-related genomes (<span><math><mrow><mo>∼</mo></mrow></math></span>30,000<em>nt</em>). We present LinearAlifold, a much faster alternative that scales linearly with both the sequence length and the number of sequences, based on our work LinearFold that folds a single RNA in linear time. Our work is orders of magnitude faster than RNAalifold (0.7 h on the above 400 genomes, or <span><math><mrow><mo>∼</mo><mn>36</mn><mo>×</mo></mrow></math></span> speedup) and achieves higher accuracies when compared to a database of known structures. More interestingly, LinearAlifold’s prediction on SARS-CoV-2 correlates well with experimentally determined structures, substantially outperforming RNAalifold. Finally, LinearAlifold supports two energy models (Vienna and BL*) and four modes: minimum free energy (MFE), maximum expected accuracy (MEA), ThreshKnot, and stochastic sampling, each of which takes under an hour for hundreds of SARS-CoV variants. Our resource is at:</p><p><span><span>https://github.com/LinearFold/LinearAlifold</span><svg><path></path></svg></span> (code) and <span><span>http://linearfold.org/linear-alifold</span><svg><path></path></svg></span> (server).</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 17","pages":"Article 168694"},"PeriodicalIF":4.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022283624002961/pdfft?md5=00f1e9455bb03b8e6b3ad40c8ff311e7&pid=1-s2.0-S0022283624002961-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544352","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
XGRm: A Web Server for Interpreting Mouse Summary-level Genomic Data XGRm:解读小鼠摘要级基因组数据的网络服务器
IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168705
Shan Wang , Chaohui Bao , Siyue Yang , Chenxu Gao , Chang Lu , Lulu Jiang , Liye Chen , Zheng Wang , Hai Fang

We introduce XGR-model (or XGRm), a web server made accessible at http://www.xgrm.pro, with the aim of meeting the increasing demand for effectively interpreting summary-level genomic data in model organisms. Currently, it hosts two enrichment analysers and two subnetwork analysers to support enrichment and subnetwork analyses for user-input mouse genomic data, whether gene-centric or genomic region-centric. The enrichment analysers identify ontology term enrichments for input genes (GElyser) or for genes linked from input genomic regions (RElyser). The subnetwork analysers rely on our previously established network algorithm to identify gene subnetworks from input gene-centric summary data (GSlyser) or from input region-centric summary data (RSlyser), leveraging network information about either functional interactions or pathway-derived interactions. Collectively, XGRm offers an all-in-one solution for gaining systems biology insights into summary-level genomic data in mice, underpinned by our commitment to regular updates as well as natural extensions to other model organisms.

我们介绍 XGR-model(或 XGRm),这是一个可在 http://www.xgrm.pro 上访问的网络服务器,旨在满足日益增长的有效解释模式生物基因组数据的需求。目前,它拥有两个富集分析器和两个子网络分析器,支持对用户输入的小鼠基因组数据(无论是以基因为中心还是以基因组区域为中心)进行富集和子网络分析。富集分析器可识别输入基因(GElyser)或输入基因组区域链接基因(RElyser)的本体术语富集。子网络分析器依赖于我们之前建立的网络算法,利用有关功能相互作用或通路衍生相互作用的网络信息,从以输入基因为中心的汇总数据(GSlyser)或以输入区域为中心的汇总数据(RSlyser)中识别基因子网络。总之,XGRm 提供了一个一体化的解决方案,让我们可以从小鼠基因组摘要数据中获得系统生物学的见解,我们承诺定期更新,并自然扩展到其他模式生物。
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引用次数: 0
E-pRSA: Embeddings Improve the Prediction of Residue Relative Solvent Accessibility in Protein Sequence E-pRSA:嵌入改进了蛋白质序列中残基相对溶剂可及性的预测
IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168494

Knowledge of the solvent accessibility of residues in a protein is essential for different applications, including the identification of interacting surfaces in protein–protein interactions and the characterization of variations. We describe E-pRSA, a novel web server to estimate Relative Solvent Accessibility values (RSAs) of residues directly from a protein sequence. The method exploits two complementary Protein Language Models to provide fast and accurate predictions. When benchmarked on different blind test sets, E-pRSA scores at the state-of-the-art, and outperforms a previous method we developed, DeepREx, which was based on sequence profiles after Multiple Sequence Alignments. The E-pRSA web server is freely available at https://e-prsa.biocomp.unibo.it/main/ where users can submit single-sequence and batch jobs.

了解蛋白质中残基的溶剂可及性对不同的应用都至关重要,包括识别蛋白质-蛋白质相互作用中的相互作用表面和表征变异。我们介绍了 E-pRSA,这是一种新型网络服务器,可直接从蛋白质序列估算残基的相对溶剂可及性值(RSA)。该方法利用两个互补的蛋白质语言模型来提供快速准确的预测。在不同的盲测试集上进行基准测试时,E-pRSA 的得分达到了最先进水平,并优于我们之前开发的基于多重序列对齐后序列剖面的 DeepREx 方法。E-pRSA 网络服务器可在 https://e-prsa.biocomp.unibo.it/main/ 免费使用,用户可以提交单序列和批处理作业。
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引用次数: 0
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures NNDB:用于预测核酸二级结构稳定性的近邻参数扩展数据库。
IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168549

Nearest neighbor thermodynamic parameters are widely used for RNA and DNA secondary structure prediction and to model thermodynamic ensembles of secondary structures. The Nearest Neighbor Database (NNDB) is a freely available web resource (https://rna.urmc.rochester.edu/NNDB) that provides the functional forms, parameter values, and example calculations. The NNDB provides the 1999 and 2004 set of RNA folding nearest neighbor parameters. We expanded the database to include a set of DNA parameters and a set of RNA parameters that includes m6A in addition to the canonical RNA nucleobases. The site was redesigned using the Quarto open-source publishing system. A downloadable PDF version of the complete resource and downloadable sets of nearest neighbor parameters are available.

近邻热力学参数被广泛用于 RNA 和 DNA 二级结构预测以及二级结构热力学集合建模。最近邻数据库(NNDB)是一个可免费获取的网络资源(https://rna.urmc.rochester.edu/NNDB),提供函数形式、参数值和计算示例。NNDB 提供了 1999 年和 2004 年的 RNA 折叠近邻参数集。我们对数据库进行了扩展,增加了一组 DNA 参数和一组 RNA 参数,其中除了典型的 RNA 核碱基外,还包括 m6A。我们使用 Quarto 开源出版系统重新设计了网站。可下载 PDF 版本的完整资源和可下载的近邻参数集。
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引用次数: 0
RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction RNA3DB:用于训练和基准测试 RNA 结构预测深度学习模型的结构相似数据集。
IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168552

With advances in protein structure prediction thanks to deep learning models like AlphaFold, RNA structure prediction has recently received increased attention from deep learning researchers. RNAs introduce substantial challenges due to the sparser availability and lower structural diversity of the experimentally resolved RNA structures in comparison to protein structures. These challenges are often poorly addressed by the existing literature, many of which report inflated performance due to using training and testing sets with significant structural overlap. Further, the most recent Critical Assessment of Structure Prediction (CASP15) has shown that deep learning models for RNA structure are currently outperformed by traditional methods.

In this paper we present RNA3DB, a dataset of structured RNAs, derived from the Protein Data Bank (PDB), that is designed for training and benchmarking deep learning models. The RNA3DB method arranges the RNA 3D chains into distinct groups (Components) that are non-redundant both with regard to sequence as well as structure, providing a robust way of dividing training, validation, and testing sets. Any split of these structurally-dissimilar Components are guaranteed to produce test and validations sets that are distinct by sequence and structure from those in the training set. We provide the RNA3DB dataset, a particular train/test split of the RNA3DB Components (in an approximate 70/30 ratio) that will be updated periodically. We also provide the RNA3DB methodology along with the source-code, with the goal of creating a reproducible and customizable tool for producing structurally-dissimilar dataset splits for structural RNAs.

随着 AlphaFold 等深度学习模型在蛋白质结构预测方面取得的进展,RNA 结构预测最近也受到了深度学习研究人员越来越多的关注。与蛋白质结构相比,实验解析的 RNA 结构更稀疏,结构多样性更低,因此 RNA 带来了巨大的挑战。现有文献往往没有很好地解决这些挑战,其中许多文献报告了由于使用了结构严重重叠的训练集和测试集而导致的性能膨胀。此外,最新的结构预测关键评估(CASP15)表明,目前 RNA 结构深度学习模型的性能优于传统方法。在本文中,我们介绍了 RNA3DB,这是一个结构化 RNA 数据集,源自蛋白质数据库(PDB),专为深度学习模型的训练和基准测试而设计。RNA3DB 方法将 RNA 三维链排列成不同的组(Components),这些组在序列和结构上都是非冗余的,从而为划分训练集、验证集和测试集提供了一种稳健的方法。对这些结构不同的组件进行任何拆分,都能保证生成的测试集和验证集在序列和结构上都不同于训练集。我们提供的 RNA3DB 数据集是 RNA3DB 组成部分的特定训练/测试拆分集(比例约为 70/30),将定期更新。我们还提供了 RNA3DB 方法和源代码,目的是创建一个可重复和可定制的工具,用于生成结构 RNA 的结构相似数据集拆分。
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引用次数: 0
CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation CHARMM-GUI PDB 阅读器和操纵器:共价配体建模与仿真
IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.jmb.2024.168554

Molecular modeling and simulation serve an important role in exploring biological functions of proteins at the molecular level, which is complementary to experiments. CHARMM-GUI (https://www.charmm-gui.org) is a web-based graphical user interface that generates complex molecular simulation systems and input files, and we have been continuously developing and expanding its functionalities to facilitate various complex molecular modeling and make molecular dynamics simulations more accessible to the scientific community. Currently, covalent drug discovery emerges as a popular and important field. Covalent drug forms a chemical bond with specific residues on the target protein, and it has advantages in potency for its prolonged inhibition effects. Even though there are higher demands in modeling PDB protein structures with various covalent ligand types, proper modeling of covalent ligands remains challenging. This work presents a new functionality in CHARMM-GUI PDB Reader & Manipulator that can handle a diversity of ligand-amino acid linkage types, which is validated by a careful benchmark study using over 1,000 covalent ligand structures in RCSB PDB. We hope that this new functionality can boost the modeling and simulation study of covalent ligands.

分子建模和模拟在分子水平探索蛋白质的生物学功能方面发挥着重要作用,是对实验的补充。CHARMM-GUI (https://www.charmm-gui.org) 是一个基于网络的图形用户界面,可生成复杂的分子模拟系统和输入文件,我们一直在不断开发和扩展其功能,以方便各种复杂的分子建模,使科学界更容易获得分子动力学模拟。目前,共价药物发现已成为一个热门的重要领域。共价药物能与目标蛋白质上的特定残基形成化学键,具有长效抑制作用的优势。尽管对带有各种共价配体类型的 PDB 蛋白结构建模提出了更高的要求,但共价配体的正确建模仍具有挑战性。本研究在 CHARMM-GUI PDB Reader & Manipulator 中提出了一种新功能,它可以处理多种配体-氨基酸连接类型,并通过使用 RCSB PDB 中超过 1000 个共价配体结构进行仔细的基准研究验证了这一功能。我们希望这一新功能能促进共价配体的建模和模拟研究。
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引用次数: 0
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