ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling

ChimeraX——用于多尺度建模的下一代可视化和分析软件

• 批准号: 10707058
• 负责人: THOMAS E FERRIN
• 金额: $ 66.47万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10707058
• 关键词: 3-Dimensional; Abate; Address; Advanced Development; Algorithms; Amino Acid Sequence; Area; Attention; Base Sequence; Biological; Biological Process; Biomedical Research; Brain; Cell physiology; Cells; Cellular Structures; Charge; Communities; Complex; Computational Biology; Computer Graphics; Computer software; Computers; Cryoelectron Microscopy; Data; Data Analyses; Data Set; Development; Disease; Docking; Documentation; Drosophila genus; Drug Design; Drug Targeting; Educational process of instructing; Electron Microscopy; Elements; Face; Feedback; Foundations; Funding; Goals; Growth; Image; Intuition; Journals; Knowledge; Length; Life; Lighting; Link; Maps; Methods; Microscopy; Modeling; Molecular; Molecular Analysis; Molecular Conformation; Molecular Machines; Molecular Structure; Mutation; Operating System; Outcome; Pattern; Performance; Process; Production; Property; Protein Engineering; Proteins; Publications; Reading; Reporting; Research; Research Personnel; Research Project Grants; Resolution; Role; Scientist; Sequence Alignment; Software Engineering; Software Tools; Source Code; Structure; Talents; Techniques; Three-dimensional analysis; Time; Tissue imaging; Tissues; Tomogram; Training; United States National Institutes of Health; Visualization; Visualization software; Work; animation; applied biomedical research; base; biological systems; complex data; density; design; drug development; experimental study; flexibility; human disease; innovation; insight; interactive tool; lectures; machine learning method; molecular assembly/self assembly; molecular dynamics; mouse model; movie; multi-scale modeling; multidimensional data; next generation; particle; precision medicine; software repository; statistics; structural biology; technology development; three-dimensional visualization; timeline; tomography; tool; virtual reality; web based software; web site

PROJECT SUMMARY/ABSTRACT The goal of this project is to enable scientific discovery and advances in biomedical research through the development of cutting-edge software tools that provide integrated visualizations and analyses of molecular structures and related biological information. Our tools can be applied to diverse types of biomolecular data, including atomic-resolution coordinates, 3D cryo-EM density maps, and protein and nucleic acid sequences, annotations, and networks. We focus on unmet software needs for basic and applied biomedical research using highly trained and talented staff, with excellent interdisciplinary knowledge and specialized, state-of-the-art expertise in software engineering, computer graphics visualization, and data analysis. Our primary efforts are in the interactive visualization and analysis of structures of molecules, molecular assemblies, and protein sequence-structure relationships. These areas are critical for addressing important and highly relevant biomedical problems such as identifying the molecular bases of disease, identifying targets for drug development, designing drugs, and engineering proteins with new functions. Our software tools enable scientists to understand, analyze, and illustrate to others the important principles of molecular structure, function, and interactions. These tools are widely recognized as works of the highest quality, and are available for free on our website in binary and source-code form. We support and maintain these tools, and provide detailed documentation and tutorials. Our technological developments are disseminated widely via scientific publications, lectures, software distribution, and video animations.

项目总结/摘要 该项目的目标是通过以下方式促进生物医学研究的科学发现和进步： 开发尖端的软件工具，提供集成的可视化和分析， 分子结构和相关的生物信息。我们的工具可以应用于各种类型的 生物分子数据，包括原子分辨率坐标，3D cryo-EM密度图和蛋白质 以及核酸序列、注释和网络。我们专注于未满足的软件需求， 和应用生物医学研究，使用训练有素和才华横溢的工作人员，具有优秀的跨学科 在软件工程、计算机图形学方面的知识和专业的、最先进的专业知识 可视化和数据分析。我们的主要工作是交互式可视化和分析 分子结构、分子组装和蛋白质序列-结构关系。这些 这些领域对于解决重要和高度相关的生物医学问题至关重要， 确定疾病的分子基础，确定药物开发的目标，设计药物， 并设计具有新功能的蛋白质。我们的软件工具使科学家能够理解， 分析，并向他人说明分子结构，功能和 交互.这些工具被广泛认为是最高质量的作品，可用于 在我们的网站上以二进制和源代码的形式免费提供。我们支持并维护这些工具， 提供详细的文档和教程。我们的技术发展被传播 通过科学出版物、讲座、软件分发和视频动画广泛传播。

项目成果

FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales.

• DOI: 10.1073/pnas.2214599119
• 发表时间: 2022-12-13
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Gaday, Quentin;Megrian, Daniela;Carloni, Giacomo;Martinez, Mariano;Sokolova, Bohdana;Ben Assaya, Mathilde;Legrand, Pierre;Brule, Sebastien;Haouz, Ahmed;Wehenkel, Anne Marie;Alzari, Pedro M.
• 通讯作者: Alzari, Pedro M.

Structural Studies Reveal that Endosomal Cations Promote Formation of Infectious Coxsackievirus A9 A-Particles, Facilitating RNA and VP4 Release.

• DOI: 10.1128/jvi.01367-22
• 发表时间: 2022-12-21
• 期刊: Journal of virology
• 影响因子: 5.4

Structural insights into the Venus flytrap mechanosensitive ion channel Flycatcher1.

• DOI: 10.1038/s41467-022-28511-5
• 发表时间: 2022-02-14
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Jojoa-Cruz S;Saotome K;Tsui CCA;Lee WH;Sansom MSP;Murthy SE;Patapoutian A;Ward AB
• 通讯作者: Ward AB

Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome.

• DOI: 10.1073/pnas.2308600120
• 发表时间: 2023-10-24
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Blikstad, Cecilia;Dugan, Eli J.;Laughlin, Thomas G.;Turnsek, Julia B.;Liu, Mira D.;Shoemaker, Sophie R.;Vogiatzi, Nikoleta;Remis, Jonathan P.;Savage, David F.
• 通讯作者: Savage, David F.

Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein.

• DOI: 10.1093/nargab/lqac101
• 发表时间: 2022-12
• 期刊: NAR GENOMICS AND BIOINFORMATICS
• 影响因子: 4.6
• 作者: Sedhom, Jacklin;Kinser, Jason;Solomon, Lee A.
• 通讯作者: Solomon, Lee A.