Development of GRAMM Method and Software for Protein-Protein Docking

蛋白质-蛋白质对接的 GRAMM 方法和软件的开发

• 批准号: 9808093
• 负责人: Ilya Vakser
• 金额: $ 30.92万
• 依托单位: Medical University of South Carolina
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-09-15 至 2001-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9808093&HistoricalAwards=false
• 关键词: Development; GRAMM; Method; Software; Protein

The main goal of this project is to obtain a method which will produce an accurate model of a protein-protein complex from two separate, flexible, and possible inaccurate protein structures. A distinguishing feature of this new docking procedure is that it searches through the conformation of each protein in addition to the relative positions of the two proteins. This project involves the further development of GRAMM (Global RAnge Molecular Matching) docking methodology and software for protein docking. GRAMM is used at low resolution to predict the structures of complexes in the non-redundant database of protein complexes using both actual individual structures from the complexes and their models. The flexible docking procedure is expected to be more accurate and more robust with respect to the inaccuracies in the initial approximate structures of the interacting proteins than are the currently prevalent rigid docking procedures. The approach will be especially useful in view of the rate of advance in the human genome project, since it will allow a rapid evaluation of functions for a large number of predicted protein structures. Thus, the combination of protein structure prediction and protein docking is expected to increase greatly the usefulness of molecular modeling.

这个项目的主要目标是获得一种方法，可以从两个独立的、灵活的、可能不准确的蛋白质结构中产生蛋白质-蛋白质复合体的准确模型。这种新的对接程序的一个显著特点是，它除了搜索两种蛋白质的相对位置外，还搜索每种蛋白质的构象。该项目涉及GRAMM(全球范围分子匹配)对接方法和蛋白质对接软件的进一步开发。GRAMM在低分辨率下被用来预测蛋白质复合体的非冗余数据库中的复合体的结构，使用来自复合体及其模型的实际个体结构。与目前流行的刚性对接程序相比，对于相互作用蛋白质的初始近似结构中的不准确，柔性对接程序有望更准确和更健壮。鉴于人类基因组计划的进展速度，该方法将特别有用，因为它将允许快速评估大量预测的蛋白质结构的功能。因此，蛋白质结构预测和蛋白质对接的结合有望极大地提高分子建模的实用性。