MSL

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.

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

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

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

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, Manus Biosynthesis, Cambridge MA

• Brett T. Hannigan, DNAnexus, Mountain View, CA

• Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, Grigoryan Lab

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:

Devin Sok, Katie J Doores, Bryan Briney, Khoa M Le, Karen L Saye-Francisco, Alejandra Ramos, Daniel W Kulp, Jean-Philippe Julien, Sergey Menis, Lalinda Wickramasinghe, Michael S Seaman, William R Schief, Ian A Wilson, Pascal Poignard, Dennis R Burton

Promiscuous glycan site recognition by antibodies to the high-mannose patch of gp120 broadens neutralization of HIV.

Sci Transl Med: 2014, 6(236);236ra63

[PubMed:24828077] ##WORLDCAT## [DOI] (I p)

Benjamin K Mueller, Sabareesh Subramaniam, Alessandro Senes

A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα-H hydrogen bonds.

Proc. Natl. Acad. Sci. U.S.A.: 2014, 111(10);E888-95

[PubMed:24569864] ##WORLDCAT## [DOI] (I p)

Brian C Smith, Eric S Underbakke, Daniel W Kulp, William R Schief, Michael A Marletta

Nitric oxide synthase domain interfaces regulate electron transfer and calmodulin activation.

Proc. Natl. Acad. Sci. U.S.A.: 2013, 110(38);E3577-86

[PubMed:24003111] ##WORLDCAT## [DOI] (I p)

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.

Meth. 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, Thomas G 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)