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<big>'''MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.'''
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=MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.=
</big>
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[[Image:MSL-logo.png|right|400px]]
 
[[Image:MSL-logo.png|right|400px]]
  
 +
'''MSL''' is a open source C++ software library for molecular modeling produced in the [http://seneslab.org '''Senes Lab'''] at the University of Wisconsin-Madison, in collaboration with a team or researchers from a number of Universities and companies.
  
 
===Philosophy===
 
===Philosophy===
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Some of the features supported by the library are:
 
Some of the features supported by the library are:
  
* Support for reading and writing PDB files.
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* 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.
 
* 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.
 
* 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.
 
* Transformations such as translations, rotations, and alignments.
* The CHARMM force field and other potential energies.
+
* The CHARMM force field and other energy funtions.
 
* Support for CHARMM topology and parameter files.
 
* Support for CHARMM topology and parameter files.
 
* Structure building from scratch (using internal coordinates)
 
* Structure building from scratch (using internal coordinates)
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* Local backbone sampling.
 
* Local backbone sampling.
 
* Crystal lattice generation.
 
* Crystal lattice generation.
* A '''[[PyMOL|PyMol Python Interface]]''' for calling MSL code from within PyMOL'.
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* 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...
 
* And more...
  
 
===Documentation===
 
===Documentation===
The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]''', '''[[MSL by example|usage examples]]''' and a structured '''[[Tutorial|tutorial]]'''.  
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The '''[[Documentation]]''' – currently still under construction – provides a description of the '''[[MSL Objects|objects]]''' and of some '''[[MSL Programs|distrubuted programs and utilites]]'''. A  step by step '''[[Tutorial|tutorial]]''' is being assembled.
  
 +
===Status===
 +
Current version: 1.1, released on April 3, 2013.
  
 
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Previous versions: 1.0, released on July 8, 2012.
===Status===
 
The libraries are in an advanced alpha stage and in active development. They are suitable for production work (at your own risk, we use them for it daily), but the APIs are not set in stone so the occasional bug will surface and feature development will be ongoing.
 
  
 
===Source===
 
===Source===
  
The source code can be downloaded on SourceForge.  Go to the '''[[Download]]''' page.
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The source code can be downloaded on SourceForge.  Go to the '''[[Tutorial:Getting_started:_Downloading_MSL|Download]]''' page.  ([[ToDo|"To do" list]]).
  
 
===Main development team:===
 
===Main development team:===
  
* [http://senes.biochem.wisc.edu '''Senes Lab, U Wisconsin-Madison''']: Alessandro Senes (senes@wisc.edu), Sabareesh Subraminiam (subramaniam2@wisc.edu)
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* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab''']
* [http://www.lanl.gov/bioscience/ '''Biosciences Division, Los Alamos National Lab''']: Dan Kulp (dwkulp@lanl.gov)
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* Dan Kulp, IAVI, Scripps Research Institute, La Jolla CA
* [http://degrado.med.upenn.edu '''DeGrado Lab, U Pennsylvania''']: Brett Hannigan (brettth@mail.med.upenn.edu), Jason Donald (jdon@mail.med.upenn.edu)
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* Jason Donald, Manus Biosynthesis, Cambridge MA
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* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
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* Gevorg Grigoryan, James Zhang, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab''']
  
 
=== Reference ===  
 
=== Reference ===  
A manuscript is currently in preparation.
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Article published using MSL should cite:
 +
<pubmed>22565567</pubmed>
 +
 
 +
'''MSL (including early versions) has been used in the following work:'''
 +
<pubmed>24828077 24569864 24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>

Revision as of 21:00, 24 May 2014

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

MSL-logo.png

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 Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group
  • 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.
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)