PALI - a database of Phylogeny and ALIgnment of homologous protein structures
PALI - a database of Phylogeny and ALIgnment of homologous protein structures
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DOI：
10.1093/nar/29.1.61
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发表时间：
2001-01-01
影响因子：
14.9
通讯作者：
Srinivasan, N
中科院分区：
文献类型：
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作者：
Balaji, S;Sujatha, S;Srinivasan, N
PALI（1.2版）包含三维（3-D）结构依赖的序列比对以及基于结构的不同家族同源蛋白结构域的系统发育树。同源蛋白结构的数据集是通过查阅SCOP数据库（1.50版）得出的，该数据集包括604个同源蛋白家族，涉及2739个蛋白结构域结构，每个家族至少由两个成员组成。家族中的每个成员在结构上都与同一家族中的其他成员对齐（成对对齐），并且家族中的所有成员也使用同时叠加对齐（多重对齐）。使用STAMP程序（版本4.2），结构比对在很大程度上是自动进行的，特别是在亲缘关系较远的蛋白质的情况下，需要人工干预。每个家族还与使用PHYLIP（版本3.5）计算的两个树形图相关联，一个基于为每个成对排列定义的结构不相似性度量，另一个基于拓扑等效残基的相似性。这些树状图可以很容易地比较一个家族成员之间基于序列和结构的关系。基于结构的比对与结构和序列相似性的细节、重叠的坐标集和树状图可以通过web界面方便地访问。该数据库可以查询序列或结构相似度在特定范围内的蛋白质对。因此，PALI形成了一个有用的资源，以帮助分析在给定的序列相似性水平上序列和结构变化之间的关系。巴利也有超过653名“孤儿”（单身家庭）。使用包含PSI BLAST和PHYLIP的web界面，可以将新蛋白质序列与PALI中的一个家族关联起来，并将查询序列与已知3-D结构的蛋白质结合起来生成系统发育树。该数据库具有web界面搜索和树形图生成工具，可通过http://pauling.mbu.iisc.ernet.in/similar访问pali。
PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain structures with each family made up of at least two members. Each member in a family has been structurally aligned with every other member in the same family (pairwise alignment) and all the members in the family are also aligned using simultaneous superposition (multiple alignment). The structural alignments are performed largely automatically, with manual interventions especially in the cases of distantly related proteins, using the program STAMP (version 4.2). Every family is also associated with two dendrograms, calculated using PHYLIP (version 3.5), one based on a structural dissimilarity metric defined for every pairwise alignment and the other based on similarity of topologically equivalent residues. These dendrograms enable easy comparison of sequence and structure-based relationships among the members in a family. Structure-based alignments with the details of structural and sequence similarities, superposed coordinate sets and dendrograms can be accessed conveniently using a web interface. The database can be queried for protein pairs with sequence or structural similarities falling within a specified range. Thus PALI forms a useful resource to help in analysing the relationship between sequence and structure variation at a given level of sequence similarity. PALI also contains over 653 'orphans' (single member families). Using the web interface involving PSI BLAST and PHYLIP it is possible to associate the sequence of a new protein with one of the families in PALI and generate a phylogenetic tree combining the query sequence and proteins of known 3-D structure. The database with the web interfaced search and dendrogram generation tools can be accessed at http://pauling.mbu.iisc.ernet.in/similar to pali.