MMM: A toolbox for integrative structure modeling.
TLDR
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.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.read more
Citations
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Journal Article
Correction for Site-directed spin labeling of a genetically encoded unnatural amino acid
Mark R. Fleissner,Eric M. Brustad,Tamás Kálai,Christian Altenbach,Duilio Cascio,Francis B. Peters,Kálmán Hideg,Sebastian Peuker,Peter G. Schultz,Wayne L. Hubbell +9 more
TL;DR: The introduction of an orthogonal labeling strategy to make SDSL amenable to any protein, i.e., one that does not rely on any of the functional groups found in the common 20 amino acids, suggests that K1 will be a useful sensor of local structure and of conformational changes in solution.
Journal ArticleDOI
The contribution of modern EPR to structural biology.
TL;DR: Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments.
Journal ArticleDOI
Benchmark test and guidelines for DEER/PELDOR experiments on nitroxide-labeled biomolecules
Olav Schiemann,Caspar A. Heubach,Dinar Abdullin,Katrin Ackermann,Mykhailo Azarkh,Elena G. Bagryanskaya,Malte Drescher,Burkhard Endeward,Jack H. Freed,Laura Galazzo,Daniella Goldfarb,Tobias Hett,Laura Esteban Hofer,Luis Fábregas Ibáñez,Eric J. Hustedt,Svetlana Kucher,Ilya Kuprov,Janet E. Lovett,Andreas Meyer,Sharon Ruthstein,Sunil Saxena,Stefan Stoll,Christiane R. Timmel,Marilena Di Valentin,Hassane S. Mchaourab,Thomas F. Prisner,Bela E. Bode,Enrica Bordignon,Marina Bennati,Gunnar Jeschke +29 more
TL;DR: In this paper, the authors define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results.
Journal ArticleDOI
Optimal Tikhonov regularization for DEER spectroscopy.
Thomas H. Edwards,Stefan Stoll +1 more
TL;DR: The results indicate that several α selection methods perform quite well, among them the Akaike information criterion and the generalized cross validation method with either the first- or second-derivative operator, significantly better than currently utilized L-curve methods.
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The extracellular gate shapes the energy profile of an ABC exporter
Cedric A. J. Hutter,M. Hadi Timachi,Lea M. Hürlimann,Iwan Zimmermann,Pascal Egloff,Hendrik Göddeke,Svetlana Kucher,Saša Štefanić,Mikko Karttunen,Lars V. Schäfer,Enrica Bordignon,Seeger +11 more
TL;DR: A synthetic single domain antibody (sybody) is generated that recognizes the heterodimeric ABC exporter TM287/288 exclusively in the presence of ATP and demonstrates that efficient extracellular gate closure is required to dissociate the NBD dimer after ATP hydrolysis to reset the transporter back to its inward-facing state.
References
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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Reduced surface: An efficient way to compute molecular surfaces
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