MMM

MMM 2020.1

An open-source program for visualization, inspection, generation, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques.

DownloadDownload MMM 2020.1 (ZIP, 191.7 MB)

MMM 2018.2

An open-source program for visualization, inspection, generation, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques. Version 2018/11/10 including RigiFlex updates, (currently undocumented) support for restrained structure optimization with Tinker, new rotamer libraries, and a "new" command for avoiding memory issues in batch processing of multiple structures by command scripts.

DownloadDownload MMM 2018.2 (ZIP, 229.8 MB)

MMM 2018.1

DownloadDownload MMM 2018.1 (ZIP, 229.7 MB)

MMM 2017.2

DownloadDownload MMM 2017.2 (ZIP, 206.8 MB)

MMM 2017.1

MMM 2015.1

MMM 2015.1 introduces modeling of intrinsically disordered domains and proteins based on long-range distance distribution restraints and optional secondary structure and bilayer immersion depth restraints. New spin label types have been added. DEER simulations and superposition of structures have been upgraded in order to work with ensembles. Limitations on the number of residues per chain and atoms per structure have been removed.

DownloadDownload MMM 2015.1 (288 Mb). (ZIP, 294.9 MB)

MMM 2014 (beta)

Password-protected beta version of MMM 2014. Stable, but some functionality is still incomplete or help files are incomplete. Adapted to the new graphics engine of Matlab 2014b that is faster for rotation and zoom. Older versions do not run on Matlab 2014b. Ask us, if you want to test.

MMM 2013.2

An open-source program for visualization, inspection, generation, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques.

Version 2013.2 introduces localization of paramagnetic centers from distance constraints, building of networks of sites from distance constraints, and rigid-body docking of homooligomers and heterodimers from distance constraints by a grid-search approach.

MMM 2013

An open-source program for visualization, inspection, generation, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques.

Version 2013 introduces an estimate of model quality for structural transitions, adapted rotamer libraries, and systematic and automated tests of rotamer libraries against experimental data. Help files for modeling of structural transitions were improved.

MMM 2011

An open-source program for visualization, inspection, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques.

Version 2011.2 improves elastic network model-based fitting of conformational changes of a protein from a structure for the initial state and a set of spin label distance constraints for the final state. Furthermore, homology modeling constrained by label-label distances is now supported (based on third-party software Modeller from the Sali lab).

Version 2011.1 allows for fitting conformational changes of a protein from a structure for the initial state and a set of spin label distance constraints for the final state. For this, a modified and adapted Zheng/Brooks algorithm based on an anisotropic elastic network model was implemented. A paper describing scope and limitations of the approach has been submitted.

DownloadDownload MMM 2011.1 (77 Mb) (ZIP, 77.9 MB)

With Version 2011 external pageStefan Stoll (University of Washington) has joined the MMM team.
A more than tenfold speed up of rotamer computation and site scan analysis is the result. Site scan output is much easier to read and navigate.
Further new functionality includes computation and analysis of elastic network models, loop reconstruction through a Modeller interface, and bundling with MUSCLE sequence alignment, which aids structure superposition.

Requires Matlab (version 7.6 or later).

useful references:

in-silico spin labelling of protein structures using rotamer library approach used in the MMM package is described in:

external pageY. Polyhach, E. Bordignon and G. Jeschke: Rotamer libraries of spin-labelled cysteins for protein studies. PCCP 13(6) (2011) 2356-2366

examples on doing rotamer library scans of the protein chains (or entire proteins) are given in:

external pageY. Polyhach and G. Jeschke: Prediction of favourable sites for spin labelling of proteins. Spectroscopy (AMSTERDAM, Netherlands) 2010, 24(6), 651-659.

MMM 2010

An open-source program for visualization, inspection, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques. Version 2010 features in-silico spin labelling, modeling of a lipid bilayer, simulation of EPR distance measurements (DEER) and ³¹P Mims ENDOR spectra, as well as a beta version of accessibility prediction (oxygen and NiEDDA via progressive power saturation measurements and water via deuterium three-pulse ESEEM).
Requires Matlab (version 7.6 or later).

MMM 2009

First patch that solves issues for PDB files with missing residues or with selenomethionine residues. The patch also allows to compute distance distributions between a nitroxide label and a metal center or two metal centers.

DownloadDownload MMM 2009 patch 1 (116 kb)