MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

By Michael Feig, John Karanicolas, Charles L. Brooks III. Journal of Molecular Graphics and Modelling, 2004

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Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs (2022, methodology): “…complex ensemble, the ternary complex ensemble is clustered using the Multiscale Modeling Tools for Structural Biology (MMTSB) clustering script (44) with an RMSD threshold of 3 Å. Models in the same cluster are considered as the same conformation and are ranked based on the ternary complex…”
Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations (2019, methodology): “Preparation for the MD simulations, pre-/post-processing of PDB files, locPREFMD was performed by the MMTSB Tool Set 47 with CHARMM.”
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 (2017, methodology): “We used for this the jclust hierarchical clustering of the MMTSB tools [21], with the maximum number of clusters set to 10 and the minimum number of structures per cluster to 4.”