Fu Biao, Sahakyan Aleksandr B, Camilloni Carlo, Tartaglia Gian Gaetano, Paci Emanuele, Caflisch Amedeo, Vendruscolo Michele, Cavalli Andrea
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom.
J Comput Chem. 2014 May 30;35(14):1101-5. doi: 10.1002/jcc.23588. Epub 2014 Mar 27.
Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.
Almost（全原子分子模拟工具包）是一个用于确定复杂分子系统（包括蛋白质和核酸）结构并进行分析的开源计算软件包。Almost的设计有两个主要目标：提供利用各种类型实验测量作为构象约束来确定分子结构的工具，以及提供分析和评估复杂分子系统结构和动力学性质的方法。Almost中包含的方法包括利用源自核Overhauser效应测量的距离约束、从残余偶极耦合获得的取向约束以及化学位移的结构约束来确定蛋白质的结构和动力学特征。在此，我们展示Almost的首个公开发布版本，突出其计算设计的关键方面，并讨论当前实现的主要特性。Almost可用于最常见的基于Unix的操作系统，包括Linux和Mac OS X。Almost根据GNU通用公共许可证免费分发，可从项目网站http://www.open-almost.org获取源代码和二进制可执行文件。感兴趣的用户可以在http://sourceforge.net/projects/almost上关注并为Almost的进一步开发做出贡献。
