PROTEIN SURFACE DATABASE W/ FAST QUERIES FOR HOMOLOGY

具有快速同源查询功能的蛋白质表面数据库

• 批准号: 6151066
• 负责人: RICHARD Masten FINE
• 金额: $ 38.78万
• 依托单位: STRUCTURAL PROTEOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 1996
• 资助国家: 美国
• 起止时间: 1996-09-15 至 2002-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6151066
• 关键词: Internet; chemical information system; computer human interaction; computer program /software; computer simulation; protein sequence; protein structure function; surface property

The need for general tools to admit facile query of the collection of information in the Protein Database has become of significant interest not only within the community of structural biology but also within the community of molecular biologists interested in using structure to elucidate sequence and structure-function relationships. While tools have been developed to implement database queries to find similar protein substructures or similar 3D constellations of residues, to date no general tools have been developed to implement queries based on similarity between protein surfaces. This seems an egregious omission: it is the shape and properties of the protein surface which impart its lock- and-key specificity and are hence responsible for function. A suite of tools for the three dimensional query, superposition, and analysis of protein surfaces would find a plethora of practical applications (outlined below), and would significantly enhance the practical value of the collection of protein structures in the Protein Database. It is the purpose of this proposal to develop such capabilities, admitting queries, visualization, and analyses of protein surfaces in terms of steric and biochemical properties. Starting points for the work will consist of the Primary Topographical Sketch for feature recognition which is well- developed in the field of Computer Vision, and the collection of biochemical surface analysis and visualization tools assembled into the popular program GRASP developed at Columbia University. Software and database tools developed in the course of this work will be commercialized. PROPOSED COMMERCIAL APPLICATION: The proposed surface database query capabilities are of potential commercial use the interpretation of function of gene products, in the modification of sequence to dictate specificity and function, in the design of drug molecules capable of discriminating targets in families of related proteins, and in the design of small-molecule and peptide mimetics which biochemically emulate a functional epitope on a protein surface.

需要通用工具来轻松查询集合 蛋白质数据库中的信息已引起人们的极大兴趣 不仅在结构生物学界，而且在 对使用结构进行研究感兴趣的分子生物学家社区 阐明序列和结构-功能关系。虽然工具有 被开发来实现数据库查询以查找相似的蛋白质 子结构或类似的 3D 残基星座，迄今为止还没有 已经开发了通用工具来实现基于 蛋白质表面之间的相似性。这似乎是一个令人震惊的遗漏：它 是蛋白质表面的形状和特性，赋予其锁定性 和键特异性，因此负责功能。 一套 三维查询、叠加、分析工具 蛋白质表面将有大量的实际应用 （概述如下），并将显着提高实用价值 蛋白质数据库中蛋白质结构的集合。它是 该提案的目的是开发此类能力，接受查询， 蛋白质表面的空间和空间可视化和分析 生化特性。这项工作的出发点将包括 用于特征识别的主要地形草图，这是很好的 在计算机视觉领域开发，并收集 生化表面分析和可视化工具组装成 哥伦比亚大学开发的流行程序 GRASP。 软件和 在这项工作过程中开发的数据库工具将是 商业化。 提议的商业应用：提议的表面数据库查询 能力具有潜在的商业用途的解释 基因产物的功能，通过修饰序列来决定 药物分子设计中的特异性和功能 区分相关蛋白质家族中的目标以及设计中的目标 生化模拟的小分子和肽模拟物 蛋白质表面的功能表位。