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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.

Original publication

DOI

10.1002/jcc.23588

Type

Journal article

Journal

J Comput Chem

Publication Date

30/05/2014

Volume

35

Pages

1101 - 1105

Keywords

CHESHIRE, Molecular simulations, NMR spectroscopy, chemical shifts, molecular dynamics, residual dipolar couplings, Molecular Dynamics Simulation, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Proteins, Software