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MSL is a C++ library that enables the computational study of macromolecules.
The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own molecular modeling methods.
Philosophy
The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design).
MSL is developed in the Senes Lab at the University of Wisconsin-Madison and by a team of developers/users from other research laboratories.
Reference:
Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A.
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).
J Comput Chem. 2012 vol. 33 pages 1645-61
Download article at http://dx.doi.org/10.1002/jcc.22968
Features
- The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
- The ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
- # The CHARMM force field and other energy functions.
- Transformations such as translations, rotations, and alignments.
- Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo., backbone sampling
- Crystal lattice generation.
- Support for rotamer libraries
- Backbone modification and generation
- Supported platforms: Linux, MacOS