PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures
PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures
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DOI：
10.1093/bioinformatics/bts691
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发表时间：
2013-02-01
期刊：
影响因子：
5.8
通讯作者：
Bordo, Domenico
中科院分区：
文献类型：
--
作者：
Gallina, Anna Maria;Bisignano, Paola;Bordo, Domenico
动机：蛋白质数据库中包含的大部分条目描述了与低分子量分子（如生理化合物或合成药物）复合的蛋白质。在许多情况下，在不同的蛋白质-配体复合物中发现相同的分子。在药物化学中，比较蛋白质结合位点以了解调节结合特异性的相互作用的兴趣越来越大，因为这种结构信息可以与生物化学或生理学性质的其他实验数据相关联，并可能有助于合理的药物设计。结果如下：这里提出的网络服务蛋白质-配体相互作用提供了一种工具，用于分析和比较与所选配体复合的同源蛋白质的结合口袋。从蛋白质数据库中存在的蛋白质-配体复合物中推导出的信息，并存储在底层database.Results：这里提出的网络服务蛋白质-配体相互作用提供了一个工具来分析和比较同源蛋白质的结合口袋与选定的配体的复合物。这些信息是从蛋白质数据库中存在的蛋白质-配体复合物中推导出来的，并存储在基础数据库中。
Motivation: A large fraction of the entries contained in the Protein Data Bank describe proteins in complex with low molecular weight molecules such as physiological compounds or synthetic drugs. In many cases, the same molecule is found in distinct protein-ligand complexes. There is an increasing interest in Medicinal Chemistry in comparing protein binding sites to get insight on interactions that modulate the binding specificity, as this structural information can be correlated with other experimental data of biochemical or physiological nature and may help in rational drug design. Results: The web service protein-ligand interaction presented here provides a tool to analyse and compare the binding pockets of homologous proteins in complex with a selected ligand. The information is deduced from protein-ligand complexes present in the Protein Data Bank and stored in the underlying database.Results: The web service protein-ligand interaction presented here provides a tool to analyse and compare the binding pockets of homologous proteins in complex with a selected ligand. The information is deduced from protein-ligand complexes present in the Protein Data Bank and stored in the underlying database.