Department of Physics and Steinbuch Centre for Computing, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany.
Bioinformatics. 2013 Nov 1;29(21):2795-6. doi: 10.1093/bioinformatics/btt478. Epub 2013 Sep 9.
Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints.
We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2.
http://sourceforge.net/projects/esbmtools/.
Supplementary data are available at Bioinformatics online.
分子动力学模拟为生物分子系统的结构和功能提供了详细的见解。因此，它们通过访问实验无法达到的状态来补充实验测量。在不同的分子动力学技术中，基于天然结构的模型 (SBM) 基于能量景观理论和最小挫折原理。通常用于蛋白质和 RNA 折叠模拟，它们将生物分子系统进行粗粒化和/或简化哈密顿量，从而实现计算要求适中，同时与实验数据高度一致。eSBMTools 简化了 SBM 的运行和评估，并在添加实验或生物信息学衍生约束方面提供了高度的灵活性。
我们提出了一个软件包，允许设置、修改和评估 RNA 和蛋白质的 SBM。实现的工作流程包括基于生物信息学衍生的蛋白质间接触信息预测蛋白质复合物，基于常见 PDB 格式的标准化蛋白质折叠模拟设置，计算反应坐标，并通过加权直方图分析方法或 phi 值进行自由能计算来评估模拟。这些模块与分子动力学模拟程序 GROMACS 接口。该软件包是开源的，用独立于架构的 Python2 编写。
http://sourceforge.net/projects/esbmtools/。
补充数据可在生物信息学在线获得。
