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| − | + | =MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.= | |
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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: | ||
| − | * Support for reading and writing PDB files. | + | * 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 | + | * 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) | ||
| Line 29: | Line 32: | ||
===Status=== | ===Status=== | ||
| − | + | Current version: 1.1, released on April 3, 2013. | |
| − | + | Previous versions: 1.0, released on July 8, 2012. | |
===Source=== | ===Source=== | ||
| Line 40: | Line 43: | ||
* Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab'''] | * Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab'''] | ||
| − | * Dan Kulp, | + | * Dan Kulp, Vaccine & Immunotherapy Center, The Wistar Institute and The University of Pennsylvania, PA [https://wistar.org/our-scientists/daniel-kulp, '''Kulp Lab'''] |
| − | * Jason Donald, | + | * Jason Donald, Manus Biosynthesis, Cambridge MA |
* Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group | * Brett Hannigan, U. of Pennsylvania, Genomics and Computational Biology Graduate Group | ||
| − | * Gevorg Grigoryan, Dept. of Computer Science, Dartmouth College, Hanover NH, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab'''] | + | * 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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<pubmed>22565567</pubmed> | <pubmed>22565567</pubmed> | ||
| − | '''MSL has been used in the following work:''' | + | '''MSL (including early versions) has been used in the following work:''' |
| − | <pubmed>22576292 22178759 21482808 21287621 21321234 21287621 20945900 20080739 19722646</pubmed | + | <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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Latest revision as of 19:39, 29 October 2018
Contents
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.
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:
