ArticlePLoS computational biology2021
Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 24 citations in OpenAlex.
- Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions.Nature communications · 2025Article
- Rigid and stable nitroxide spin label for high-resolution distance measurements on proteins by DEER experiments.Magnetic resonance letters · 2025Article
- ProGuide: a flexible framework for modeling global conformational rearrangements in proteins using DEER-derived distance restraints.bioRxiv : the preprint server for biology · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data.Journal of structural biology · 2025Article
- Review
- Modeling of Cu(II)-based protein spin labels using rotamer libraries.Physical chemistry chemical physics : PCCP · 2024Article
- Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility.Nature communications · 2023Article
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling.PLoS computational biology · 2023Article
- Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches.Biomolecules · 2022Review
- Comparative evaluation of spin-label modeling methods for protein structural studies.Biophysical journal · 2022Article
- Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- Dynamical interplay between the human high-affinity copper transporter hCtr1 and its cognate metal ion.Biophysical journal · 2022Article
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.