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

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).

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

Features

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...

Documentation

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.

Status

Version 1.0 of MSL was released on July 8, 2012, which is suitable for production.

The libraries are in an advanced are in active development, and a development version is also available (use it at your own risk).

Source

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, IAVI, Scripps Research Institute, La Jolla CA
• Jason Donald, Agrivida, Inc., Medford MA
• Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
• Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, Grigoryan Lab

We have applied to the Google Summer of Code 2013. Please see this page Google_Summer_of_Code_Ideas

Reference

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:

Loren M LaPointe, Keenan C Taylor, Sabareesh Subramaniam, Ambalika Khadria, Ivan Rayment, Alessandro Senes
Structural organization of FtsB, a transmembrane protein of the bacterial divisome.
Biochemistry: 2013, 52(15);2574-85
[PubMed:23520975] ##WORLDCAT## [DOI] (I p)

Jian Zhang, Gevorg Grigoryan
Mining tertiary structural motifs for assessment of designability.
Methods Enzymol: 2013, 523;21-40
[PubMed:23422424] ##WORLDCAT## [DOI] (I p)

Amanda J Reig, Marcos M Pires, Rae Ana Snyder, Yibing Wu, Hyunil Jo, Daniel W Kulp, Susan E Butch, Jennifer R Calhoun, Thomas Szyperski, Edward I Solomon, William F DeGrado
Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins.
Nat Chem: 2012, 4(11);900-6
[PubMed:23089864] ##WORLDCAT## [DOI] (I p)

Sabareesh Subramaniam, Alessandro Senes
An energy-based conformer library for side chain optimization: improved prediction and adjustable sampling.
Proteins: 2012, 80(9);2218-34
[PubMed:22576292] ##WORLDCAT## [DOI] (I p)

Yong Ho Kim, Jason E Donald, Gevorg Grigoryan, George P Leser, Alexander Y Fadeev, Robert A Lamb, William F DeGrado
Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5.
Proc Natl Acad Sci U S A: 2011, 108(52);20992-7
[PubMed:22178759] ##WORLDCAT## [DOI] (I p)

Ivan V Korendovych, Daniel W Kulp, Yibing Wu, Hong Cheng, Heinrich Roder, William F DeGrado
Design of a switchable eliminase.
Proc Natl Acad Sci U S A: 2011, 108(17);6823-7
[PubMed:21482808] ##WORLDCAT## [DOI] (I p)

Jason E Donald, Yao Zhang, Giacomo Fiorin, Vincenzo Carnevale, David R Slochower, Feng Gai, Michael L Klein, William F DeGrado
Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion.
Proc Natl Acad Sci U S A: 2011, 108(10);3958-63
[PubMed:21321234] ##WORLDCAT## [DOI] (I p)

Jason E Donald, Daniel W Kulp, William F DeGrado
Salt bridges: geometrically specific, designable interactions.
Proteins: 2011, 79(3);898-915
[PubMed:21287621] ##WORLDCAT## [DOI] (I p)

Ivan V Korendovych, Alessandro Senes, Yong Ho Kim, James D Lear, H Christopher Fry, Michael J Therien, J Kent Blasie, F Ann Walker, William F Degrado
De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.
J Am Chem Soc: 2010, 132(44);15516-8
[PubMed:20945900] ##WORLDCAT## [DOI] (I p)

Bryan W Berger, Daniel W Kulp, Lisa M Span, Jessica L DeGrado, Paul C Billings, Alessandro Senes, Joel S Bennett, William F DeGrado
Consensus motif for integrin transmembrane helix association.
Proc Natl Acad Sci U S A: 2010, 107(2);703-8
[PubMed:20080739] ##WORLDCAT## [DOI] (I p)

Yao Zhang, Daniel W Kulp, James D Lear, William F DeGrado
Experimental and computational evaluation of forces directing the association of transmembrane helices.
J Am Chem Soc: 2009, 131(32);11341-3
[PubMed:19722646] ##WORLDCAT## [DOI] (I p)