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MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.


MSL is a open source C++ software library for molecular modeling produced in the Senes Lab at the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies.


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).

The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own methods.


Some of the features supported by the library are:

  • Support for reading and writing PDB and CRD files.
  • The ability of storing and switching between multiple atom coordinates, for conformational changes and rotameric representation of side chain conformational freedom.
  • For protein design, the ability to build and store multiple residue identities (i.e. LEU, ILE, ALA) at a position and switch between them.
  • Support for rotamer libraries.
  • Transformations such as translations, rotations, and alignments.
  • The CHARMM force field and other energy funtions.
  • Support for CHARMM topology and parameter files.
  • Structure building from scratch (using internal coordinates)
  • Search algorithms such as Monte Carlo, Dead End Elimination, and Self Consistent Mean Field Monte Carlo.
  • Local backbone sampling.
  • Crystal lattice generation.
  • A PyMOL Python Interface for calling MSL code from within PyMOL.
  • A R Interface for calling arbitrary R algorithms or plotting routines from within MSL
  • And more...


The Documentation – currently still under construction – provides a description of the objects and of some distrubuted programs and utilites. A step by step tutorial is being assembled.


Current version: 1.1, released on April 3, 2013.

Previous versions: 1.0, released on July 8, 2012.


The source code can be downloaded on SourceForge. Go to the Download page. ("To do" list).

Main development team:

  • Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, Senes Lab
  • Dan Kulp, Vaccine & Immunotherapy Center, The Wistar Institute and The University of Pennsylvania, PA Kulp Lab
  • Jason Donald, Manus Biosynthesis, Cambridge MA
  • Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
  • Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, Grigoryan Lab


Article published using MSL should cite:

Daniel W Kulp, Sabareesh Subramaniam, Jason E Donald, Brett T Hannigan, Benjamin K Mueller, Gevorg Grigoryan, Alessandro Senes
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).
J Comput Chem: 2012, 33(20);1645-61
[PubMed:22565567] ##WORLDCAT## [DOI] (I p)

MSL (including early versions) has been used in the following work: