Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
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DOI：
10.1093/bioinformatics/btz107
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发表时间：
2019-09-15
期刊：
影响因子：
5.8
通讯作者：
Naidoo, Kevin J.
中科院分区：
文献类型：
--
作者：
Senapathi, Tharindu;Bray, Simon;Naidoo, Kevin J.
动机：从基因组学到蛋白质组学，再到生物化学过程的分子描述，这一途径使药物和生物材料的发现成为可能。需要一个基因组学和蛋白质组学共同的研究框架来进行生物分子模拟，将生物数据与酶和蛋白质的动态分子机制联系起来。新手生物分子建模者面临着艰巨的任务，复杂的设置和无数可能的选择阻止他们使用分子模拟和他们进行可靠和可重复计算的能力，这些计算可以与合作者共享并验证程序的准确性。生物分子反应和相互作用动力学全球环境（BRIDGE）在Galaxy平台上开发，通过NAMD、GROMACS和CHARMM等常用软件包的工作流程和管道，实现蛋白质的基本分子动力学。BRIDGE可用于建立和模拟生物大分子，根据轨迹数据进行构象分析，并使用统计严格性对大规模蛋白质运动进行数据分析。我们说明了基本的桥梁模拟和分析能力，以前报道的CBH1蛋白质模拟。
Motivation: The pathway from genomics through proteomics and onto a molecular description of biochemical processes makes the discovery of drugs and biomaterials possible. A research framework common to genomics and proteomics is needed to conduct biomolecular simulations that will connect biological data to the dynamic molecular mechanisms of enzymes and proteins. Novice biomolecular modelers are faced with the daunting task of complex setups and a myriad of possible choices preventing their use of molecular simulations and their ability to conduct reliable and reproducible computations that can be shared with collaborators and verified for procedural accuracy.Results: We present the foundations of Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) developed on the Galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages, such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor. We illustrate the basic BRIDGE simulation and analytics capabilities on a previously reported CBH1 protein simulation.