CDD: a curated Entrez database of conserved domain alignments
CDD: a curated Entrez database of conserved domain alignments
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DOI：
10.1093/nar/gkg087
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发表时间：
2003-01-01
影响因子：
14.9
通讯作者：
Bryant, SH
中科院分区：
文献类型：
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作者：
Marchler-Bauer, A;Anderson, JB;Bryant, SH
保守域数据库（CDD）现在在Entrez系统中作为一个单独的数据库进行索引，并与MEDLINE(R)等其他Entrez数据库相连。例如，用户可以通过名称搜索域类型，或者查看Entrez序列数据库中任何蛋白质的域结构。CDD可以在万维网上访问http: / / www。ncbi。nlm。国家卫生研究院。Gov / entrez/ queryfcgi吗?Db = cdd。用户也可以使用CD-Search服务来识别新序列中的保守域，网址为http://:/www。ncbi。nlm。国家卫生研究院。gov /结构/ cdd / wrpsb.cgi。CD-Search结果和Entrez蛋白数据库中预先计算的链接使用RPS-BLAST算法和从CDD比对中导出的位置特异性评分矩阵（PSSMs）计算。cd搜索也默认运行蛋白质蛋白质查询提交到BLAST 1在http: / / www。ncbi。nlm。国家卫生研究院。gov /爆炸。CDD反映了公开可用的领域校准集合SMART和PFAM，现在还包含NCBI策划的校准模型。结构信息用于识别可能存在于所有家族成员中的核心亚结构，并产生与结构保守一致的序列比对。这个对齐模型允许NCBI管理员注释对应于家庭成员之间保存的功能站点的列。
The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez s sequence database. CDD can be accessed on the WorldWide Web at http: / / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi? db = cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http: / / www. ncbi. nlm. nih. gov/ Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez s protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein protein queries submitted to BLAST 1 at http: / / www. ncbi. nlm. nih. gov/ BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate columns corresponding to functional sites conserved among family members.