Conservation of Interaction Patterns in Protein Families

蛋白质家族中相互作用模式的保守

基本信息

  • 批准号:
    9506278
  • 负责人:
  • 金额:
    $ 30万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    1995
  • 资助国家:
    美国
  • 起止时间:
    1995-10-01 至 1998-09-30
  • 项目状态:
    已结题

项目摘要

9506278 Godzik Modeling of protein structures by computer, before it is determined experimentally, is an invaluable tool, aiding drug design, mutation studies and often structure determination itself. The main goal of this research is to improve existing tools for the modeling of protein structures by including extra information obtained from the new type of analysis of regularities in known protein structures. This whole approach can be best described as the reverse- engineering of protein structures on the computer. Protein structures will be "decomposed" into interacting fragments, and, by utilizing a library of "parts", they will be rebuilt. To gain experience as well as to measure progress during the method development, known structures will be modeled onto structures of other proteins from their structural families. Experience gained in the "rebuilding" of known structures will be used to make structural predictions for a number of real targets. %%% The main scientific trust in this research is to explore and utilize a new, interaction based, description of proteins. In such a description, a protein is seen as a collection of interactions between side chains, rather than as a set of points in space; thus, the very features responsible for the folding to a particular structure are directly used in the structure description itself. The quality of protein models obtained by homology modeling will be improved by using insights obtained through this new perspective, by focusing on side-chain interactions which remain constant with sequence changes even as protein backbone shifts and slides. The goals of this research will be achieved in two stages. In the first stage, traditional modeling techniques will be supplemented by additional information obtained from the analysis of protein families. In the second stage, a new modeling approach will be developed, where the predicted protein structure will be built inside-out, around interacting clusters of res idues, using fragments of structures from other proteins. To assist in achieving these goals, a set of necessary tools will be developed. A number of specific objectives, including building models of proteins with various levels of homology to the target, will be used to judge the progress of the research. ***
在实验确定之前,用计算机对蛋白质结构进行建模是一种非常宝贵的工具,有助于药物设计、突变研究和结构确定本身。本研究的主要目标是通过包含从已知蛋白质结构的新型规律分析中获得的额外信息来改进现有的蛋白质结构建模工具。这整个方法可以被最好地描述为在计算机上对蛋白质结构进行逆向工程。蛋白质结构将被“分解”成相互作用的片段,并利用“零件”库进行重建。为了获得经验以及测量方法开发过程中的进展,将已知结构建模到其结构家族中的其他蛋白质的结构上。在“重建”已知结构中获得的经验将用于对许多实际目标进行结构预测。这项研究的主要科学信任是探索和利用一种新的、基于相互作用的蛋白质描述。在这种描述中,蛋白质被视为侧链之间相互作用的集合,而不是空间中的一组点;因此,负责折叠到特定结构的特性直接用于结构描述本身。通过使用通过这一新视角获得的见解,通过关注侧链相互作用,通过同源建模获得的蛋白质模型的质量将得到改善,即使在蛋白质主链移动和滑动时,侧链相互作用也会随着序列变化而保持不变。本研究的目标将分两个阶段实现。在第一阶段,传统的建模技术将被从蛋白质家族分析中获得的额外信息所补充。在第二阶段,将开发一种新的建模方法,其中预测的蛋白质结构将由内而外构建,围绕相互作用的残基簇,使用来自其他蛋白质的结构片段。为了协助实现这些目标,将开发一套必要的工具。一些特定的目标,包括建立与目标具有不同程度同源性的蛋白质模型,将被用来判断研究的进展。***

项目成果

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Adam Godzik其他文献

Structural systems biology: from bacterial to cancer networks
  • DOI:
    10.1186/1471-2164-15-s2-o14
  • 发表时间:
    2014-01-01
  • 期刊:
  • 影响因子:
    3.700
  • 作者:
    Adam Godzik
  • 通讯作者:
    Adam Godzik
Correction for Burra et al., Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
Burra 等人的修正,从 PDB 中的冗余模型导出的构象状态的全局分布指出蛋白质结构的非唯一性
Evolution of the protein domain repertoire of eukaryotes reveals strong functional patterns
  • DOI:
    10.1186/gb-2010-11-s1-p43
  • 发表时间:
    2010-01-01
  • 期刊:
  • 影响因子:
    9.400
  • 作者:
    Christian M Zmasek;Adam Godzik
  • 通讯作者:
    Adam Godzik
Unusual structural and functional features of TpLRR/BspA-like LRR proteins.
TpLRR/BspA 样 LRR 蛋白的异常结构和功能特征。
  • DOI:
  • 发表时间:
    2023
  • 期刊:
  • 影响因子:
    3
  • 作者:
    Abraham Takkouche;Xinru Qiu;Mayya Sedova;L. Jaroszewski;Adam Godzik
  • 通讯作者:
    Adam Godzik
Database searching by flexible protein structure alignment
通过灵活的蛋白质结构比对进行数据库搜索
  • DOI:
  • 发表时间:
    2004
  • 期刊:
  • 影响因子:
    8
  • 作者:
    Yuzhen Ye;Adam Godzik
  • 通讯作者:
    Adam Godzik

Adam Godzik的其他文献

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{{ truncateString('Adam Godzik', 18)}}的其他基金

EAGER: Using Search Engines to Track Impact of Unsung Heroes of Big Data Revolution, Data Creators
EAGER:使用搜索引擎追踪大数据革命无名英雄、数据创建者的影响
  • 批准号:
    1931895
  • 财政年份:
    2018
  • 资助金额:
    $ 30万
  • 项目类别:
    Standard Grant
EAGER: Using Search Engines to Track Impact of Unsung Heroes of Big Data Revolution, Data Creators
EAGER:使用搜索引擎追踪大数据革命无名英雄、数据创建者的影响
  • 批准号:
    1565233
  • 财政年份:
    2015
  • 资助金额:
    $ 30万
  • 项目类别:
    Standard Grant
I-Corps: Market Research, Customer Interviews, and Customer Discovery for Novel Cancer Biomarkers
I-Corps:新型癌症生物标志物的市场研究、客户访谈和客户发现
  • 批准号:
    1559647
  • 财政年份:
    2015
  • 资助金额:
    $ 30万
  • 项目类别:
    Standard Grant
Flexible Protein Structure Alignment Program and Server
灵活的蛋白质结构比对程序和服务器
  • 批准号:
    0349600
  • 财政年份:
    2004
  • 资助金额:
    $ 30万
  • 项目类别:
    Standard Grant

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基于interaction和backbone的NP类MAS问题解集表示、复杂性统计与高效算法研究
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社交网络中异构交互模式的模型和推论
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