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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:

Michael C E Niemann, Henriette Weber, Tomáš Hluska, Georgeta Leonte, Samantha M Anderson, Ondřej Novák, Alessandro Senes, Tomáš Werner
The Cytokinin Oxidase/Dehydrogenase CKX1 Is a Membrane-Bound Protein Requiring Homooligomerization in the Endoplasmic Reticulum for Its Cellular Activity.
Plant Physiol: 2018, 176(3);2024-2039
[PubMed:29301955] ##WORLDCAT## [DOI] (I p)

Samson G F Condon, Deena-Al Mahbuba, Claire R Armstrong, Gladys Diaz-Vazquez, Samuel J Craven, Loren M LaPointe, Ambalika S Khadria, Rahul Chadda, John A Crooks, Nambirajan Rangarajan, Douglas B Weibel, Aaron A Hoskins, Janice L Robertson, Qiang Cui, Alessandro Senes
The FtsLB subcomplex of the bacterial divisome is a tetramer with an uninterrupted FtsL helix linking the transmembrane and periplasmic regions.
J Biol Chem: 2018, 293(5);1623-1641
[PubMed:29233891] ##WORLDCAT## [DOI] (I p)

Samantha M Anderson, Benjamin K Mueller, Evan J Lange, Alessandro Senes
Combination of Cα-H Hydrogen Bonds and van der Waals Packing Modulates the Stability of GxxxG-Mediated Dimers in Membranes.
J Am Chem Soc: 2017, 139(44);15774-15783
[PubMed:29028318] ##WORLDCAT## [DOI] (I p)

Xiao Guo, Natalie M Niemi, Paul D Hutchins, Samson G F Condon, Adam Jochem, Arne Ulbrich, Alan J Higbee, Jason D Russell, Alessandro Senes, Joshua J Coon, David J Pagliarini
Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function.
Cell Rep: 2017, 18(2);307-313
[PubMed:28076776] ##WORLDCAT## [DOI] (I p)

Zhi Zhang, Sabareesh Subramaniam, Justin Kale, Chenyi Liao, Bo Huang, Hetal Brahmbhatt, Samson G F Condon, Suzanne M Lapolla, Franklin A Hays, Jingzhen Ding, Feng He, Xuejun C Zhang, Jianing Li, Alessandro Senes, David W Andrews, Jialing Lin
BH3-in-groove dimerization initiates and helix 9 dimerization expands Bax pore assembly in membranes.
EMBO J: 2016, 35(2);208-36
[PubMed:26702098] ##WORLDCAT## [DOI] (I p)

Guolin Ma, Ming Wei, Lian He, Chongxu Liu, Bo Wu, Shenyuan L Zhang, Ji Jing, Xiaowen Liang, Alessandro Senes, Peng Tan, Siwei Li, Aomin Sun, Yunchen Bi, Ling Zhong, Hongjiang Si, Yuequan Shen, Minyong Li, Mi-Sun Lee, Weibin Zhou, Junfeng Wang, Youjun Wang, Yubin Zhou
Inside-out Ca(2+) signalling prompted by STIM1 conformational switch.
Nat Commun: 2015, 6;7826
[PubMed:26184105] ##WORLDCAT## [DOI] (I e)

Ambalika S Khadria, Benjamin K Mueller, Jonathan A Stefely, Chin Huat Tan, David J Pagliarini, Alessandro Senes
A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3.
J Am Chem Soc: 2014, 136(40);14068-77
[PubMed:25216398] ##WORLDCAT## [DOI] (I p)

Sabareesh Subramaniam, Alessandro Senes
Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL).
Proteins: 2014, 82(11);3177-87
[PubMed:25212195] ##WORLDCAT## [DOI] (I p)

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)