Database of Protein Modifications: Enhancements for Visualization, Modeling and Internet Access

由玛格丽特·戴霍夫在国家生物医学研究基金会(NBRF)建立的蛋白质信息资源(PIR)合作收集和出版了PIR国际蛋白质序列数据库，这是最古老的生物分子序列和注释数据库。作为其建立全面、准确、精确和一致的蛋白质序列数据库的努力的一部分，PIR维护着许多辅助注释数据库。Resid构建了一个修饰氨基酸残基的原型辅助数据库，该数据库在PIR蛋白质序列数据库中标注为特征。在注释者和外部专家的咨询下，RESID数据库提供了比蛋白质序列数据库中可能提供的更详细的化学信息、伴随蛋白质序列数据库中的特征的适当注释以及计算修饰多肽的正确分子量的方法。它也被用作自动检查特征记录中的语法和词汇的标准。它是唯一公开的、人类和计算机可读的全面记录蛋白质结构修饰的数据库，已被认为是通过质谱学鉴定翻译后修饰多肽的有用资源。拟议的两年努力的目标是：进行必要的增强，使RESID能够在互联网上访问，为数据库构建分子描述，使其能够以图形方式呈现，并协助研究人员生成翻译后修饰多肽的分子模型，以及将显示修饰残基的化学结构的软件与现有的序列数据库访问程序相结合。当这个项目完成后，增强型RESID数据库将为ATLAS和PIR万维网的用户提供以前没有的可视化显示和分子建模信息，这是蛋白质翻译后修饰的全面集合。它还将支持PIR与布鲁克海文蛋白质数据库等其他生物分子结构数据库之间的互操作性。摘要1998年7月25日1

The Protein Information Resource (PIR), established at the National Biomedical Research Foundation (NBRF) by Margaret Dayhoff, collaboratively collects and publishes the PIR International Protein Sequence Database, the oldest database of biomolecular sequences and annotation. As part of its effort to produce a protein sequence database that is comprehensive, accurate, precise and consistent, the PIR maintains a number of auxiliary annotation databases. RESID a prototype auxiliary database was constructed for modified amino acid residues annotated as features in the PIR Protein Sequence Database. Consulted by annotators and outside experts the RESID Database provides more detailed chemical information than is possible in the protein sequence database, appropriate annotations to accompany features in the Protein Sequence Database, and a means to calculate correct molecular weights for modified peptides. It is also used as the standard for automatic checking of syntax and vocabulary in feature records. It is the only publicly available, human- and computer-readable database comprehensively documenting protein structural modifications, and has been recognized as a resource useful in identifying post-translationally modified peptides by mass-spectroscopy. The objectives of the proposed two-year effort are: to undertake the enhancements necessary to make RESID accessible on the Intemet, to construct molecular descriptions for the database that will enable graphical presentation and assist researchers in generating molecular models of post-translationally modified peptides, and to integrate software that will display the chemical structure of modified residues with existing sequence database access programs. When this project is completed, the enhanced RESID Database will provide users of ATLAS and the PIR World Wide Web Site with visual display and molecular modeling information not previously available, a comprehensive collection of protein post-translational modifications. It will also support interoperability between the PIR and other biomolecular structural databases such as the Brookhaven Protein Databank. Abstract July 25, 1998 1