PROTEIN SURFACE DATABASE WITH FAST QUERIES FOR HOMOLOGY

描述：(改编自申请人的摘要)开发一种便携、 对基于Web的环境进行了表征和详细比较 提出了蛋白质表面的概念。将利用五个主要组成部分：1.a 网络服务器(向非专业用户提供表面查看功能)；2 a 数据库(由经处理的PDB文件组成)；3.一套比较工具； 4.选定家族内蛋白质的详细特征，以及5.a 新颖的查询引擎。鉴于重要功能可以不同的事实 值得注意的是，研究蛋白质表面已被证明是困难的。 以供辨认和比较。为了应对这一困难，调查人员 我采用了来自计算机的分层地形初步草图(TPS 允许不同程度的表面平滑的视觉。提取的特征 此层次结构中的对象用于对曲面进行“标记化”。这样提供的代币 对应于可按地形自然排序的要素 显赫。TPS组织数据库，该数据库包含完整 对下表面斑块的生化/生物物理描述。这将使 丰富的描述符规范，可用于数据库中的匹配 查询并允许对蛋白质中的表面进行有意义的比较 家人。将使用GRAPH程序来扩展曲面可视化 功能，并与服务器的查询引擎和底层 数据库。因此，将为用户提供及时的工具来进行 和内部结构-功能关系的解释和比较 横跨蛋白质家族。这个搜索引擎将对新兴的 结构基因组学领域。 建议的商业应用：不可用

DESCRIPTION: (adapted from applicant's abstract) Development of a facile, web-based environment for the characterization and detailed comparison of protein surfaces is proposed. Five principal components will be utilized: 1. a web server (providing surface viewing capabilities to non-expert users); 2 a database (consisting of processed PDB files); 3. a suite of comparison tools ; 4. a detailed characterization of proteins within selected families, and 5. a novel query engine. Given the fact that important features can differ significantly in prominence, it has proven difficult to study protein surfaces for recognition and comparison. To deal with this difficulty, the investigators have adopted a hierarchical topographical primary sketch (TPS) from computer vision that permits varying degrees of surface smoothing. Features extracted from this hierarchy are used to 'tokenize' the surface. The tokens so provided correspond to features that can be naturally ranked by topographical prominence. The TPS organize a database that contains a full biochemical/biophysical description of underlying surface patches. This enables a rich specification of descriptors that can be used for matching in database queries and allows for meaningful comparison of surfaces within protein families. The program GRASP will be used to extend the surface visualization capabilities, and coupled to the server's query engines and underlying databases. Thus, the user will be provided with a timely tool for the interpretation and comparison of structure-function relationships within and across protein families. This search engine will be important to the emerging field of structural genomics. PROPOSED COMMERCIAL APPLICATION: NOT AVAILABLE