ArticleProtein science : a publication of the Protein Society2018
MMM: A toolbox for integrative structure modeling.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed.
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- Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters.Nature communications · 2026Article
- Protocol for preparing and characterizing samples for combined microsecond freeze-hyperquenching and electron paramagnetic resonance spectroscopy.STAR protocols · 2026Article
- Characterization of flexible RNA binding by tandem RNA recognition motifs through integrative ensemble modelling.Nucleic acids research · 2026Article
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
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- EPR Techniques to Probe Insertion and Conformation of Spin-Labeled Proteins in Lipid Bilayers.Methods in molecular biology (Clifton, N.J.) · 2026Article
- CW ESR spectroscopy and protein spin labeling in membrane biology.Physical biology · 2025Review
- Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions.Nature communications · 2025Article
- ProGuide: a flexible framework for modeling global conformational rearrangements in proteins using DEER-derived distance restraints.bioRxiv : the preprint server for biology · 2025Article
- A short intrinsically disordered region at KtrB's N-terminus facilitates allosteric regulation of KNature communications · 2025Article
- The LptC transmembrane helix undergoes a rigid body movement upon LptBProtein science : a publication of the Protein Society · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Exploring the Structural Dynamics of LeuT Using EPR Spectroscopy: A Focus on Transmembrane Helix 10.Journal of neurochemistry · 2025Article
- The mycobacterial ABC transporter IrtAB employs a membrane-facing crevice for siderophore-mediated iron uptake.Nature communications · 2025Article
- Multistate kinetics of the syringe-like injection mechanism of Tc toxins.Science advances · 2025Article
- Pulsed EPR Methods in the Angstrom to Nanometre Scale Shed Light on the Conformational Flexibility of a Fluoride Riboswitch.Angewandte Chemie (International ed. in English) · 2024Article
- Alternating access of a bacterial homolog of neurotransmitter: sodium symporters determined from AlphaFold2 ensembles and DEER spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
31 more citing papers are in PubMed but not listed here.
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Abstract
Structural characterization of proteins and their complexes may require integration of restraints from various experimental techniques. MMM (Multiscale Modeling of Macromolecules) is a Matlab-based open-source modeling toolbox for this purpose with a particular emphasis on distance distribution restraints obtained from electron paramagnetic resonance experiments on spin-labelled proteins and nucleic acids and their combination with atomistic structures of domains or whole protomers, small-angle scattering data, secondary structure information, homology information, and elastic network models. MMM does not only integrate various types of restraints, but also various existing modeling tools by providing a common graphical user interface to them. The types of restraints that can support such modeling and the available model types are illustrated by recent application examples.
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