PISCES: recent improvements to a PDB sequence culling server.
PISCES: recent improvements to a PDB sequence culling server.
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DOI：
10.1093/nar/gki402
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发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Dunbrack RL Jr
中科院分区：
文献类型：
--
作者：
Wang G;Dunbrack RL Jr
PISCES是一个数据库服务器，用于使用许多条目和链特异性标准以及相互序列同一性从蛋白质数据库（PDB）产生序列列表。我们挑选PDB的目标是提供满足序列同一性和结构质量截止值的最高分辨率结构的可能的最长列表。新的PISCES服务器使用PSI-BLAST和基于结构的比对的组合来确定序列身份。结构比对产生更完整的比对，因此比PSI-BLAST更准确的序列同一性。PISCES现在允许用户除了按单个链进行标准剔除之外，还可以按条目剔除PDB。在这种情况下，列表将仅包含不具有与列表中的任何其他条目中的任何链在序列同一性截止上具有序列同一性的链的条目。PISCES还提供了完整注释的序列，包括基因名称和物种。服务器允许用户挑选条目或链的输入列表，以便可以使用其他标准，例如函数。在重新设计的RCSB网站上搜索PDB的结果可以通过单击输入PISCES服务器，将PDB的强大搜索能力与PISCES的序列剔除实用程序相结合。服务器的数据每周更新一次。服务器位于。
PISCES is a database server for producing lists of sequences from the Protein Data Bank (PDB) using a number of entry- and chain-specific criteria and mutual sequence identity. Our goal in culling the PDB is to provide the longest list possible of the highest resolution structures that fulfill the sequence identity and structural quality cut-offs. The new PISCES server uses a combination of PSI-BLAST and structure-based alignments to determine sequence identities. Structure alignment produces more complete alignments and therefore more accurate sequence identities than PSI-BLAST. PISCES now allows a user to cull the PDB by-entry in addition to the standard culling by individual chains. In this scenario, a list will contain only entries that do not have a chain that has a sequence identity to any chain in any other entry in the list over the sequence identity cut-off. PISCES also provides fully annotated sequences including gene name and species. The server allows a user to cull an input list of entries or chains, so that other criteria, such as function, can be used. Results from a search on the re-engineered RCSB's site for the PDB can be entered into the PISCES server by a single click, combining the powerful searching abilities of the PDB with PISCES's utilities for sequence culling. The server's data are updated weekly. The server is available at .
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影响因子：
14.9
作者：
Wheeler DL;Church DM;Edgar R;Federhen S;Helmberg W;Madden TL;Pontius JU;Schuler GD;Schriml LM;Sequeira E;Suzek TO;Tatusova TA;Wagner L
通讯作者：
Wagner L
影响因子：
14.9
作者：
Westbrook, J;Feng, ZK;Berman, HM
通讯作者：
Berman, HM
DOI：
10.1093/protein/11.9.739
发表时间：
1998-09-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
Shindyalov, IN;Bourne, PE
通讯作者：
Bourne, PE
影响因子：
14.9
作者：
THOMPSON, JD;HIGGINS, DG;GIBSON, TJ
通讯作者：
GIBSON, TJ
影响因子：
5.6
作者：
Sadreyev, R;Grishin, N
通讯作者：
Grishin, N