Difference between revisions of "Main Page"

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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.=
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</big>
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[[Image:MSL-logo.png|right|400px]]
 
[[Image:MSL-logo.png|right|400px]]
  
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'''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:
  
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* 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.
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* Support for rotamer libraries.
 
* Transformations such as translations, rotations, and alignments.
 
* Transformations such as translations, rotations, and alignments.
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* The CHARMM force field and other potential energies.
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* 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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===Status===
 
===Status===
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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.
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Current version: 1.1, released on April 3, 2013.
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Previous versions: 1.0, released on July 8, 2012.
  
 
===Source===
 
===Source===
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===Main development team:===
 
===Main development team:===
  
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* [http://senes.biochem.wisc.edu '''Senes Lab, U Wisconsin-Madison''']: Alessandro Senes (senes _AT_ wisc.edu), Sabareesh Subraminiam (subramaniam2 _AT_ 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''']
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* [http://www.scripps.edu '''The Scripps Research Institute, La Jolla, Ca''']: Dan Kulp (dwkulp _AT_ scripps.edu)
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* Dan Kulp, Vaccine & Immunotherapy Center, The Wistar Institute and The University of Pennsylvania, PA [https://wistar.org/our-scientists/daniel-kulp, '''Kulp Lab''']
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* [http://degrado.med.upenn.edu '''DeGrado Lab, U Pennsylvania''']: Brett Hannigan (brettth _AT_ mail.med.upenn.edu), Jason Donald (jdon _AT_ 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 ===  
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A primary manuscript is currently in preparation.
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Article published using MSL should cite:
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<pubmed>22565567</pubmed>
  
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'''MSL in the literature'''
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'''MSL (including early versions) has been used in the following work:'''
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<pubmed>21482808</pubmed>
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<pubmed>29301955 29233891 29028318 28076776 26702098 26184105 25216398 25212195 24828077 24569864 24003111 23520975 23422424 23089864 22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed>
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<pubmed>21321234</pubmed>
 
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<pubmed>20080739</pubmed>
 
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<pubmed>19722646</pubmed>
 

Latest revision as of 19:39, 29 October 2018

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, 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

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:

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