Looking for a mentor -- multiscale molecular modeling package MMB (and molmodel)

[Samuel Flores <samuelfloresc@gmail.com>]

Dear Debian Mentors,

I would like some help packaging MacroMoleculeBuilder (MMB) for distribution in Debian or Ubuntu. It is a mature piece of code, used to publish many scientific articles in structural bioinformatics and structural and molecular biology. It has been downloaded thousands of times.

MacroMoleculeBuilder (MMB) is a multiscale, internal-coordinate modeling package which I have been developing since 2007. It was originally written to model Ribonucleic Acid (RNA) folding, and was the first to perform homology modeling of RNA, though it can do the same for complexes including RNA, DNA, and protein. It performs fitting to low-resolution density maps (such as those produced by Cryo-Electron Microscopy), attaining speedups of three orders of magnitude compared to related methods, particularly for very large complexes such as the ribosome.  It peforms template docking, in which two monomers are brought into their bound conformation using the coordinates of a related complex. It performs morphing, meaning interpolation of  intermediates between two known protein conformations, at higher speed and with better accuracy than prior methods; the method can be applied to much larger complexes than previously reported. One reason to use MMB in a Bioinformatics course is that because it is so diverse in its possible applications, the student only needs to learn one package to perform most of the required modeling tasks. As it offers the student direct control over the modeling process, it better communicates the underlying methodology, compared to single-purposes codes or web servers. Because it is multifunctional, it is also possible to perform integrative modeling, meaning that several different features can be combined to address a unique problem or question. I would be happy to change MMB's license to be compatible with this process.

MMB requires OpenMM, simbody, and SeqAn, I believe all of these are already packaged. It also requires SimTK molmodel which is not packaged -- I am the maintainer of molmodel and would like to package this as well. Molmodel is not hard to compile, but it does use cmake. 

I would be most grateful for any help received in this process.

With kind regards,

Sam