ADFR: A Modular Software Framework for Docking into Flexible Receptors

ADFR:用于对接灵活受体的模块化软件框架

基本信息

  • 批准号:
    9239951
  • 负责人:
  • 金额:
    $ 39.66万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2011
  • 资助国家:
    美国
  • 起止时间:
    2011-04-15 至 2020-06-30
  • 项目状态:
    已结题

项目摘要

Project Summary/Abstract Automated docking is an important tool for gaining a mechanistic understanding of the molecular interactions underpinning most biological processes. It supports biomedical applications ranging from drug and chemical probes design to investigating chemical pathways and identifying therapeutic targets for diseases such as cancer and metabolic disorders. Two major challenges for automated docking remain the conformational changes occurring in macromolecules upon ligand binding and the docking highly flexible ligands such as peptides, an area that has gained a lot of interest recently. Most docking programs use rigid models of macromolecules because of the exponential increase of computational complexity and the decreased docking accuracy associated receptor flexibility. Under the previous award, we made significant progress towards docking with flexible receptors. We developed and released a software program allowing the successful cross- docking of flexible ligands into apo conformations of receptors with up to 14 flexible side-chains, and demonstrated that down-weighting the contribution of the receptor internal energy to the scoring function increased docking success rates. For the next award, we propose to: 1) extend the set of motion objects for describing ligand conformational changes beyond rotatable bonds, and motion objects for representing local and global receptor backbone motions such as flexible loops and domain motions; 2) enhance our current search technique and develop a new representation and associate search technique for docking peptides; 3) calibrate and optimize the scoring function sused during docking specifically in the context of docking with receptor flexibility; and 4) make the software useful and usable through clearly written documentation and intuitive graphical user interfaces. Datasets compiled under this project will also be made freely available to the community and provide a benchmark for evaluating docking methods. This Open-Source software development project will be based on best practices in software engineering and result in a modular, component-based software environment with pluggable search techniques and scoring functions, and an extensible set of molecular flexibility descriptors. This new docking engine will be part of the widely used and popular software suite AutoDock. It will be used on the World Community Grid for large virtual screens on therapeutically important targets. The ability to include receptor flexibility in docking simulations will extend the range of biological problems for which automated docking can be successfully applied. Hence, it will impact the research of many medicinal chemists and biologist, and extend the use of computational tools to a wider community of scientists thereby supporting the advancement of biomedical research.
项目总结/文摘

项目成果

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MICHEL F. SANNER其他文献

MICHEL F. SANNER的其他文献

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{{ truncateString('MICHEL F. SANNER', 18)}}的其他基金

In-silico prediction of protein-peptide interactions.
蛋白质-肽相互作用的计算机预测。
  • 批准号:
    10116950
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
VISUALIZATION AND VISUAL WORKFLOW ENVIRONMENT TO ENHANCE MULTI-SCALE MODELING
可视化和可视化工作流程环境增强多尺度建模
  • 批准号:
    8362789
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
In-silico prediction of protein-peptide interactions.
蛋白质-肽相互作用的计算机预测。
  • 批准号:
    10432107
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
In-silico prediction of protein-peptide interactions.
蛋白质-肽相互作用的计算机预测。
  • 批准号:
    10259801
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
AutoDock-FR: A Modular Approach to Flexible Receptor Docking
AutoDock-FR:灵活受体对接的模块化方法
  • 批准号:
    8449664
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
AutoDock-FR: A Modular Approach to Flexible Receptor Docking
AutoDock-FR:灵活受体对接的模块化方法
  • 批准号:
    8635369
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
AutoDock-FR: A Modular Approach to Flexible Receptor Docking
AutoDock-FR:灵活受体对接的模块化方法
  • 批准号:
    8255452
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
In-silico prediction of protein-peptide interactions.
蛋白质-肽相互作用的计算机预测。
  • 批准号:
    10653086
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
AutoDock-FR: A Modular Approach to Flexible Receptor Docking
AutoDock-FR:灵活受体对接的模块化方法
  • 批准号:
    8076706
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:
AutoDock-FR: A Modular Approach to Flexible Receptor Docking
AutoDock-FR:灵活受体对接的模块化方法
  • 批准号:
    8824945
  • 财政年份:
    2011
  • 资助金额:
    $ 39.66万
  • 项目类别:

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