Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).

Journal of Computational Chemistry
Daniel W KulpAlessandro Senes

Abstract

We present the Molecular Software Library (MSL), a C++ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduce...Continue Reading

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Citations

Oct 24, 2012·Nature Chemistry·Amanda J ReigWilliam F DeGrado
Sep 5, 2013·Proceedings of the National Academy of Sciences of the United States of America·Brian C SmithMichael A Marletta
Feb 27, 2014·Proceedings of the National Academy of Sciences of the United States of America·Benjamin K MuellerAlessandro Senes
Jul 18, 2015·Nature Communications·Guolin MaYubin Zhou
Nov 22, 2014·Bioinformatics·Layla HirshSilvio C E Tosatto
Jun 9, 2016·Biophysical Journal·Gina-Mirela MustataMeni Wanunu
Nov 28, 2013·Biopolymers·Marina FaiellaGiovanna Ghirlanda
Oct 14, 2017·Journal of the American Chemical Society·Samantha M AndersonAlessandro Senes
Mar 26, 2013·Biochemistry·Loren M LaPointeAlessandro Senes
Sep 13, 2014·Journal of the American Chemical Society·Ambalika S KhadriaAlessandro Senes

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