ALMOST: An all atom molecular simulation toolkit for protein structure determination. Issue 14 (27th March 2014)

• Record Type: Journal Article
• Authors: Fu, Biao; Sahakyan, Aleksandr B.; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea
• Is Part Of: Journal of computational chemistry. Volume 35:Issue 14(2014)
• Page Start: 1101
• Page End: 1105
• Publication Date: 2014-03-27
• Subjects: Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.23588
• Languages: English
• ISSNs: 0192-8651

Abstract

<abstract abstract-type="main"> <title> <x xml:space="preserve">Abstract</x> </title> <p> <bold>Almost</bold> (<bold>al</bold>l atom <bold>mo</bold>lecular <bold>s</bold>imulation <bold>t</bold>oolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. <bold>Almost</bold> 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 <bold>Almost</bold> 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 <bold>Almost</bold>, highlight the key aspects of its computational design and discuss the main features currently implemented. <bold>Almost</bold> is available for the most common Unix‐based operating systems, including Linux and Mac OS X. <bold>Almost</bold> 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 <ext-link ext-link-type="uri" xlink:href="http://www.open-almost.org" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.open‐almost.org</ext-link>. Interested users can follow and contribute to the further development of <bold>Almost</bold> on <ext-link ext-link-type="uri" xlink:href="http://sourceforge.net/projects/almost" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">http://sourceforge.net/projects/almost</ext-link>. © 2014 Wiley Periodicals, Inc.</p> </abstract>