MSL-Libraries wiki_msl_libraries_org http://msl-libraries.org/index.php?title=Main_Page MediaWiki 1.32.6 first-letter Media Special Talk User User talk MSL Libraries MSL Libraries talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 1 904 901 2018-10-29T19:39:22Z Senes 2 wikitext text/x-wiki =MSL: an open source C++ library for analysis, manipulation, modeling and design of macromolecules.= [[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=== 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 '''[[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. Previous versions: 1.0, released on July 8, 2012. ===Source=== 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:=== * Alessandro Senes, Sabareesh Subraminiam, Ben Mueller, Dept. of Biochemistry, U. of Wisconsin-Madison, [http://senes.biochem.wisc.edu '''Senes Lab'''] * 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, 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, [http://www.cs.dartmouth.edu/~gevorg/ '''Grigoryan Lab'''] === Reference === Article published using MSL should cite: <pubmed>22565567</pubmed> '''MSL (including early versions) has been used in the following work:''' <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> 401icowf2v4umtybztcuk44tkfp460u