Valuev Vadim P, Afonnikov Dmitry A, Ponomarenko Mikhail P, Milanesi Luciano, Kolchanov Nikolay A
Institute of Cytology and Genetics, Lavrentieva ave. 10, Novosibirsk 630090, Russia and Istituto Tecnologie Biomediche Avanzate, Via Fratelli Cervi 93, 20090 Segrate, Italy.
Nucleic Acids Res. 2002 Jan 1;30(1):200-2. doi: 10.1093/nar/30.1.200.
ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution processes (mainly by means of phage display). At present, the ASPD database contains data on 195 selection experiments, which were described in 112 original papers. For each experiment, the following information is given: (i) description of the target for binding, (ii) description of the protein or peptide which serves as the template for library construction and description of the native protein which binds the target, (iii) links to the major proteomic databases (SWISS-PROT, PDB, PROSITE and ENZYME), (iv) keywords referring to the biological significance of the experiment, (v) aligned sequences of proteins or peptides retrieved through in vitro evolution and relevant native or constructed sequences, (vi) the number of rounds of selection/amplification and (vii) the number of occurrences of clones with each sequence. The literature data include a full reference, a link to the MEDLINE database and the name of the corresponding author with his email address. ASPD has a user-friendly interface which allows for simple queries using the names of proteins and ligands, as well as keywords describing the biological role of the interaction studied, and also for queries based on authors' names. It is also possible to access the database by means of the SRS system, allowing complex queries. There is a BLAST search tool against the ASPD for looking directly for homologous sequences. Research tools of the ASPD allow the analysis of pairwise correlations in the sequences of proteins and peptides selected against one target. The URL for the ASPD database is http://www.sgi.sscc.ru/mgs/gnw/aspd/.
ASPD是一个新的精选数据库，它整合了通过体外定向进化过程（主要通过噬菌体展示）获得的全长蛋白质、蛋白质结构域和肽的数据。目前，ASPD数据库包含195个筛选实验的数据，这些数据在112篇原始论文中有所描述。对于每个实验，给出了以下信息：(i) 结合靶标的描述；(ii) 作为文库构建模板的蛋白质或肽的描述以及与靶标结合的天然蛋白质的描述；(iii) 与主要蛋白质组数据库（SWISS-PROT、PDB、PROSITE和ENZYME）的链接；(iv) 涉及实验生物学意义的关键词；(v) 通过体外进化检索到的蛋白质或肽的比对序列以及相关的天然或构建序列；(vi) 筛选/扩增的轮数；(vii) 每个序列的克隆出现次数。文献数据包括完整的参考文献、到MEDLINE数据库的链接以及相应作者的姓名和电子邮件地址。ASPD具有用户友好的界面，允许使用蛋白质和配体的名称以及描述所研究相互作用生物学作用的关键词进行简单查询，也允许基于作者姓名进行查询。还可以通过SRS系统访问该数据库，进行复杂查询。有一个针对ASPD的BLAST搜索工具，用于直接查找同源序列。ASPD的研究工具允许分析针对一个靶标筛选出的蛋白质和肽序列中的成对相关性。ASPD数据库的网址是http://www.sgi.sscc.ru/mgs/gnw/aspd/ 。
