Protein-ligand binding sites. Identification, characterization and interrelations
Protein-ligand binding sites. Identification, characterization and interrelations
复制标题
蛋白质-配体结合位点。
DOI：
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发表时间：
2011
期刊：
影响因子：
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通讯作者：
Peter Schmidtke
中科院分区：
文献类型：
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作者：
Peter Schmidtke
动机：各种口袋检测算法现在可以免费或商业化地提供给科学界用于分析静态蛋白质结构。然而，由于蛋白质是动态的实体，提高这些程序的能力，直接检测和表征腔考虑蛋白质构象合奏应该是有价值的捕获口袋的可塑性，因此允许深入了解结构-功能关系。结果如下：本文介绍了一种新的方法，称为MDpocket，提供了一个快速，免费和开源的工具，用于跟踪小分子的结合位点和气体迁移路径的MD轨迹或其他构象合奏。MDpocket基于fpocket空腔检测算法，是对现有分析工具的宝贵贡献。MDpocket的能力示出了三个相关的情况下：i）使用HSP 90的晶体结构的合奏瞬时子口袋的检测，ii）已知的氙结合位点和肌红蛋白中的迁移途径的检测，和iii）识别合适的口袋P38地图激酶的分子对接。可用性：MDpocket是免费的开源软件，可以在http://fpocket.sourceforge.net下载。联系方式：pschmidtke@ub.edu补充信息：补充数据可从生物信息学在线网站获得。
Motivation: A variety of pocket detection algorithms are now freely or commercially available to the scientific community for the analysis of static protein structures. However, since proteins are dynamic entities, enhancing the capabilities of these programs for the straightforward detection and characterization of cavities taking into account protein conformational ensembles should be valuable for capturing the plasticity of pockets, and therefore allow gaining insight into structure-function relationships. Results: This paper describes a new method, called MDpocket, providing a fast, free and open source tool for tracking small molecule binding sites and gas migration pathways on MD trajectories or other conformational ensembles. MDpocket is based on the fpocket cavity detection algorithm and a valuable contribution to existing analysis tools. The capabilities of MDpocket are illustrated for three relevant cases: i) the detection of transient sub-pockets using an ensemble of crystal structures of HSP90 ii) the detection of known xenon binding sites and migration pathways in myoglobin, and iii) the identification of suitable pockets for molecular docking in P38 Map kinase. Availability: MDpocket is free and open source software and can be downloaded at http://fpocket.sourceforge.net. Contact: pschmidtke@ub.edu Supplementary information: Supplementary data are available at Bioinformatics online.