Integrated Resource for Nucleic Acid Structures

核酸结构综合资源

• 批准号: 10696121
• 负责人: Craig L Zirbel
• 金额: $ 37.18万
• 依托单位: BOWLING GREEN STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-10 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10696121
• 关键词: 3-Dimensional; Atlases; Automated Annotation; Base Pairing; Base Sequence; Biological; Cell physiology; Cells; Classification; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Complex; Controlled Vocabulary; Cryoelectron Microscopy; DNA; DNA Binding; DNA Structure; Data; Data Discovery; Data Reporting; Data Set; Deposition; Drug Design; Drug Targeting; Elements; Gene Expression Regulation; Genes; Genetic Recombination; Genetic Transcription; Geometry; Human body; Hybrids; Link; Location; Maps; Mediating; Methods; Modeling; Molecular Conformation; Names; Nucleic Acid Databases; Nucleic Acid Resources; Nucleic Acids; Physiological Processes; Play; Positioning Attribute; Process; Protein Analysis; Proteins; Publishing; RNA; RNA Recognition Motif; RNA-Binding Proteins; Recurrence; Replication Origin; Reporting; Research Personnel; Resources; Ribosomes; Role; Scheme; Shapes; Signal Transduction; Source; Specificity; Structure; System; Time; Untranslated RNA; Visualization; Work; data resource; ds-DNA; experience; genetic information; genetic regulatory protein; improved; innovation; interest; knowledge base; nanomachine; nucleic acid binding protein; nucleic acid structure; protein complex; repaired; three dimensional structure; tool; transcription factor; transmission process; trend

SUMMARY We are analyzing, annotating, organizing, and integrating nucleic acid 3D structural data with sequence and functional data and delivering it to biomedical researchers. The significance of the proposal lies in the prominent roles of nucleic acids in a host of cellular and physiological processes, mediated by interaction with specific DNA- and RNA-binding proteins. DNA encodes genetic information and takes part in replication, recombination, transcription, and repair. RNA transmits genetic information and takes part in all aspects of gene regulation. RNA is also the key component of the ribosome, the universal protein-making nano-machine and an important target for drug design. RNA/DNA hybrids occur in many biological contexts, including transcription complexes, origins of replication, and the widely heralded CRISPR-CAS systems for precision editing of genes (Wright 2016). They form unique structures different from double helical RNA or DNA. High throughput methods have catalogued many new non-coding RNAs (ncRNAs) and RNA-binding proteins lacking previously known RNA-binding domains. The Specific Aims of this proposal are: 1) Create more complete annotations for all nucleic acid 3D structures, 2) create new annotations for nucleic acid-protein complexes, and 3) create a Nucleic Acid Knowledge Base (NAKB) that allows for both deep and wide searching of information about nucleic acid sequences and structures. Under these aims, we will analyze and annotate all types of nucleic acid 3D structures, including DNA, RNA, and DNA/RNA hybrids, and improve our ability to predict 3D structures from sequence. The NAKB resource will provide new search capabilities, enhanced reports, and link-outs to external data, features and tools. The proposed enhancements will greatly improve our abilities to search and visualize existing data on nucleic acid sequence and structural features and will further enrich the user experience and enable data discovery. The innovation of the proposal is the creation of a unified resource for all nucleic acid 3D structures.

概括 我们正在分析，注释，组织和整合核酸3D结构数据与序列和 功能数据并将其传递给生物医学研究人员。该提议的意义在于杰出的 核酸在许多细胞和生理过程中的作用，通过与特定DNA-的相互作用介导 和RNA结合蛋白。 DNA编码遗传信息并参与复制，重组， 转录和维修。 RNA传递遗传信息，并参与基因调节的各个方面。 RNA 也是核糖体，通用蛋白质制造纳米机器的关键组成部分和重要目标 用于药物设计。 RNA/DNA杂种发生在许多生物学环境中，包括转录复合物，起源 复制，以及广泛的基因精确编辑的CRISPR-CAS系统（Wright 2016）。他们 形成与双螺旋RNA或DNA不同的独特结构。高通量方法已分类 许多新的非编码RNA（NCRNA）和RNA结合蛋白缺乏以前已知的RNA结合 域。该提案的具体目的是：1）为所有核酸3D创建更完整的注释 结构，2）为核酸 - 蛋白质复合物创建新的注释，3）创建核酸 知识库（NAKB）允许对核酸的信息进行深入和广泛的搜索 序列和结构。在这些目标下，我们将分析和注释所有类型的核酸3D结构， 包括DNA，RNA和DNA/RNA杂种，并提高我们从序列预测3D结构的能力。 NAKB资源将提供新的搜索功能，增强报告以及与外部数据的链接， 功能和工具。提出的增强功能将大大提高我们搜索和可视化现有的能力 核酸序列和结构特征的数据，将进一步丰富用户体验并启用 数据发现。该提案的创新是为所有核酸3D创建统一资源 结构。

项目成果

The Nucleic Acid Database: new features and capabilities.

• DOI: 10.1093/nar/gkt980
• 发表时间: 2014-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Coimbatore Narayanan B;Westbrook J;Ghosh S;Petrov AI;Sweeney B;Zirbel CL;Leontis NB;Berman HM
• 通讯作者: Berman HM

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure.

• DOI: 10.1371/journal.pone.0139900
• 发表时间: 2015
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Theis C;Zirbel CL;Zu Siederdissen CH;Anthon C;Hofacker IL;Nielsen H;Gorodkin J
• 通讯作者: Gorodkin J

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.

• DOI: 10.1093/nar/gkw453
• 发表时间: 2016-07-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Roll J;Zirbel CL;Sweeney B;Petrov AI;Leontis N
• 通讯作者: Leontis N

The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.

• DOI: 10.1093/nar/gkad957
• 发表时间: 2024-01-05
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Lawson, Catherine L.;Berman, Helen M.;Chen, Li;Vallat, Brinda;Zirbel, Craig L.
• 通讯作者: Zirbel, Craig L.

Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.

• DOI: 10.1021/jp204820b
• 发表时间: 2011-09
• 期刊: The journal of physical chemistry. A
• 作者: Marie Zgarbová;P. Jurečka;P. Banáš;M. Otyepka;J. Šponer;N. Leontis;Craig L. Zirbel;Jiřı́ Šponer