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MSALigMap - 一种将PDB结构中的活性位点氨基酸映射到具有相似功能的已知和新型未注释同源序列上的工具。

MSALigMap-A Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function.

作者信息

Hassan Sameer, Haleemath Sameer Sameena, Töpel Mats, Aronsson Henrik

机构信息

Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 461, 405 30 Gothenburg, Sweden.

OlsAro Crop Biotech AB, Erik Dahlbergsgatan 11A, 411 26 Gothenburg, Sweden.

出版信息

Life (Basel). 2022 Dec 12;12(12):2082. doi: 10.3390/life12122082.

DOI:10.3390/life12122082
PMID:36556447
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9784966/
Abstract

MSALigMap (Multiple Sequence Alignment Ligand Mapping) is a tool for mapping active-site amino-acid residues that bind selected ligands on to target protein sequences of interest. Users can also provide novel sequences (unavailable in public databases) for analysis. MSALigMap is written in Python. There are several tools and servers available for comparing and mapping active-site amino-acid residues among protein structures. However, there has not previously been a tool for mapping ligand binding amino-acid residues onto protein sequences of interest. Using MSALigMap, users can compare multiple protein sequences, such as those from different organisms or clinical strains, with sequences of proteins with crystal structures in PDB that are bound with the ligand/drug and DNA of interest. This allows users to easily map the binding residues and to predict the consequences of different mutations observed in the binding site. The MSALigMap server can be accessed at https://albiorix.bioenv.gu.se/MSALigMap/HomePage.py.

摘要

MSALigMap（多序列比对配体映射）是一种用于将结合选定配体的活性位点氨基酸残基映射到目标蛋白质序列上的工具。用户还可以提供新的序列（公共数据库中没有的）进行分析。MSALigMap是用Python编写的。有几种工具和服务器可用于比较和映射蛋白质结构中的活性位点氨基酸残基。然而，以前还没有一种工具可以将配体结合氨基酸残基映射到感兴趣的蛋白质序列上。使用MSALigMap，用户可以将多个蛋白质序列，如来自不同生物体或临床菌株的序列，与PDB中结合了感兴趣的配体/药物和DNA的具有晶体结构的蛋白质序列进行比较。这使得用户能够轻松地映射结合残基，并预测在结合位点观察到的不同突变的后果。可通过https://albiorix.bioenv.gu.se/MSALigMap/HomePage.py访问MSALigMap服务器。

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Ligand Binding Site Comparison - LiBiSCo - a web-based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites.配体结合位点比较 - LiBiSCo - 一个基于网络的工具，用于分析蛋白质和配体之间的相互作用，以探索活性位点内的氨基酸特异性。
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