Continued Development and Maintenance of the UltraScan Software

UltraScan 软件的持续开发和维护

• 批准号: 10673959
• 负责人: Emre H. Brookes
• 金额: $ 29.31万
• 依托单位: UNIVERSITY OF MONTANA
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10673959
• 关键词: APBA1 gene; Address; Aging; Algorithms; Anisotropy; Antineoplastic Agents; Architecture; Australia; Biochemistry; Biomedical Research; Biophysics; Biopolymers; CRISPR/Cas technology; Canada; Cellular biology; Code; Collaborations; Communities; Complex; Computer software; Data; Data Analyses; Data Protection; Data Security; Databases; Development; Diffusion; Dimensions; Disease; Drug Targeting; Ensure; Europe; Finland; Fluorescence; Funding; Future; HIV; High Performance Computing; India; Infrastructure; Institution; Intuition; Investigation; Kinetics; Laboratories; Libraries; Licensing; Linux; Maintenance; Malignant Neoplasms; Management Information Systems; Measures; Medicine; Methods; Modernization; Molecular; Molecular Structure; Network-based; Neurodegenerative Disorders; Neutrons; Nucleic Acids; Operating System; Peer Review; Property; Publications; Reaction; Records; Research; Resolution; Resources; Roentgen Rays; Science; Services; Side; Small Interfering RNA; Spectrum Analysis; Supercomputing; Support System; System; Systems Analysis; Techniques; Training; United States National Institutes of Health; Update; Viral Vector; Work; X-Ray Crystallography; analytical ultracentrifugation; automated analysis; base; beamline; biophysical analysis; code development; data acquisition; density; design; drug testing; experimental study; flexibility; high throughput analysis; improved; instrument; instrumentation; lipid nanoparticle; macromolecular assembly; materials science; middleware; models and simulation; nanoscience; novel; open source; operation; simulation; software development; structural biology; supercomputer; therapeutic development; tool; two-dimensional; user protection; vector

Project Summary/Abstract We propose to continue development and support for the UltraScan-III (US3) software suite and develop new code and methods to address challenging biomedical research questions that can be solved with the latest instruments available for analytical ultracentrifugation and at beamlines for small-angle X-ray and neutron scattering experiments (SAXS/SANS) experiments. UltraScan is a comprehensive toolkit for the analysis of data from hydrodynamic experiments and simulations. Such experiments include analytical ultracentrifugation, SAXS/SANS, as well as bead modeling simulations. Support for this project will assure continued availability of a mature multi-platform analysis suite with important and unique capabilities not found in any other software packages. Chief among them are tight integration of supercomputing capabilities, LIMS support for collaboration, and specialized analysis routines. US3 enjoys widespread use in the AUC and SAXS/SANS communities, and offers the most robust optimization and simulation algorithms available, resulting in unmatched detail. UltraScan provides the highest throughput, a flexible, modern GUI, and a comprehensive list of analysis routines. Proposed developments include automated data acquisition and analysis workflows, improvements in the fitting of floating data, improved two-dimensional grids, support for density distribution analysis critical for the accurate characterization and quantification of viral vectors, lipid nanoparticles loaded with cancer drugs or nucleic acids, and other vectors used for the delivery of medicines or CRISPR technology.

项目摘要/摘要 我们建议继续开发和支持超声-III(US3)软件套件，并开发新的 解决具有挑战性的生物医学研究问题的代码和方法，这些问题可以通过最新的 可用于分析性超速离心机和用于小角X射线和中子的光束线仪器 散射实验(SAXS/SANS)实验。超声仪是一个全面的工具包，用于分析 水动力实验和模拟的数据。这类实验包括分析性超速离心法， SAXS/SANS，以及胎圈建模模拟。对该项目的支持将确保持续提供 成熟的多平台分析套件，具有任何其他软件所没有的重要且独特的功能 包裹。其中最主要的是超级计算能力的紧密集成，LIMS支持 协作和专门的分析例程。US3在AUC和SAXS/SANS中广泛使用 社区，并提供可用的最健壮的优化和模拟算法，导致 无与伦比的细节。超声波提供最高的吞吐量、灵活的现代图形用户界面和全面的列表 分析例行程序。拟议的发展包括自动化数据获取和分析工作流程， 改进了浮动数据的拟合，改进了二维网格，支持密度分布 分析对病毒载体、载脂纳米粒的准确表征和定量至关重要 使用抗癌药物或核酸，以及用于运送药物或CRISPR技术的其他载体。

项目成果

Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism.

• DOI: 10.1038/s41467-021-22253-6
• 发表时间: 2021-03-31
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Horne CR;Venugopal H;Panjikar S;Wood DM;Henrickson A;Brookes E;North RA;Murphy JM;Friemann R;Griffin MDW;Ramm G;Demeler B;Dobson RCJ
• 通讯作者: Dobson RCJ

Shape2SAS: a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes.

• DOI: 10.1107/s1600576723005848
• 发表时间: 2023-08-01
• 期刊: JOURNAL OF APPLIED CRYSTALLOGRAPHY
• 影响因子: 6.1
• 作者: Larsen, Andreas Haahr;Brookes, Emre;Pedersen, Martin Cramer;Kirkensgaard, Jacob Judas Kain
• 通讯作者: Kirkensgaard, Jacob Judas Kain

Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures.

超越 US-SOMO-AF 数据库：一个新网站，用于对用户提供的结构进行流体动力学、结构和圆二色性计算。

• DOI: 10.1007/s00249-023-01636-1
• 发表时间: 2023
• 期刊: European biophysics journal : EBJ
• 作者: Brookes,EmreH;Rocco,Mattia
• 通讯作者: Rocco,Mattia

MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks.

• DOI: 10.1371/journal.pcbi.1011749
• 发表时间: 2024-01
• 期刊: PLoS computational biology
• 影响因子: 4.3

Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom.

抗嗜蛋蛋白DM64的分子结构及其与Bothrops Asper毒液中肌毒素II的结合特异性。

• DOI: 10.3389/fmolb.2021.787368
• 发表时间: 2021
• 期刊: Frontiers in molecular biosciences
• 影响因子: 5
• 作者: Soares BS;Rocha SLG;Bastos VA;Lima DB;Carvalho PC;Gozzo FC;Demeler B;Williams TL;Arnold J;Henrickson A;Jørgensen TJD;Souza TACB;Perales J;Valente RH;Lomonte B;Gomes-Neto F;Neves-Ferreira AGC
• 通讯作者: Neves-Ferreira AGC