Web服务器
鉴定(生物学)
钥匙(锁)
职位(财务)
计算机科学
路径(计算)
可视化
最短路径问题
接口(物质)
变构调节
数据挖掘
理论计算机科学
互联网
万维网
化学
生物
酶
图形
生物化学
植物
计算机安全
财务
气泡
最大气泡压力法
并行计算
经济
程序设计语言
作者
Guillem Casadevall,Jordi Casadevall,Cristina Duran,Sílvia Osuna
出处
期刊:Protein Engineering Design & Selection
[Oxford University Press]
日期:2024-01-01
卷期号:37
被引量:7
标识
DOI:10.1093/protein/gzae005
摘要
Abstract SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally-relevant positions of a given enzyme structure and dynamics. The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. We provide in this publication information on how to generate the files for SPM construction even for non-expert users and discuss the most relevant parameters that can be modified. The tool is extremely fast (it takes less than one minute per job), thus allowing the rapid identification of distal positions connected to the active site pocket of the enzyme. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community. SPMweb is freely available for academia at http://spmosuna.com/.
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