MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
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DOI：
10.1016/j.jmgm.2003.12.005
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发表时间：
2004-05-01
影响因子：
2.9
通讯作者：
Brooks, CL
中科院分区：
文献类型：
--
作者：
Feig, M;Karanicolas, J;Brooks, CL
我们描述了用于结构生物学的多尺度建模工具（MMTSB）工具集（http：mmtsb.scripps.edu/software/mmtsbToolSet. HTML），它是一组新颖的实用程序和编程库，为蛋白质和核酸的模拟提供了新的增强的采样和多尺度建模技术。该工具集接口与现有的分子建模包CHARMM和琥珀经典的全原子模拟，并与MONSTER基于晶格的低分辨率构象采样。此外，它还为两个详细级别之间的集成和转换添加了新功能。副本交换方法的实施，以允许增强采样的全原子和低分辨率模型。该工具集旨在结构生物学中的应用，涉及蛋白质或核酸结构预测，细化和/或扩展构象采样。考虑到结构预测应用程序，该工具集还实现了一个设施，允许控制和应用建模任务的一个大的构象，我们称之为合奏计算。Ensemble计算包括高端并行计算机上的松散耦合并行计算、集群计算网格和桌面网格环境.本文描述了MMTSB工具集的设计和实现，并通过三个典型的例子说明了它的实用性：对一组预测的蛋白质构象进行评分，以识别最接近天然结构的结构，用复制交换法在隐式溶剂中从头折叠肽，以及预测较大蛋白质结构中的缺失片段。(C)2004年爱思唯尔公司All rights reserved.
We describe the Multiscale Modeling Tools for Structural Biology (MMTSB) Tool Set (http://mmtsb.scripps.edu/software/mmtsbToolSet. html), which is a novel set of utilities and programming libraries that provide new enhanced sampling and multiscale modeling techniques for the simulation of proteins and nucleic acids. The tool set interfaces with the existing molecular modeling packages CHARMM and Amber for classical all-atom simulations, and with MONSSTER for lattice-based low-resolution conformational sampling. In addition, it adds new functionality for the integration and translation between both levels of detail. The replica exchange method is implemented to allow enhanced sampling of both the all-atom and low-resolution models. The tool set aims at applications in structural biology that involve protein or nucleic acid structure prediction, refinement, and/or extended conformational sampling. With structure prediction applications in mind, the tool set also implements a facility that allows the control and application of modeling tasks on a large set of conformations in what we have termed ensemble computing. Ensemble computing encompasses loosely coupled, parallel computation on high-end parallel computers, clustered computational grids and desktop grid environments.This paper describes the design and implementation of the MMTSB Tool Set and illustrates its utility with three typical examples-scoring of a set of predicted protein conformations in order to identify the most native-like structures, ab initio folding of peptides in implicit solvent with the replica exchange method, and the prediction of a missing fragment in a larger protein structure. (C) 2004 Elsevier Inc. All rights reserved.