ArticleBiophysical journal2011
Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- ModeHunter: A Package for the Reductionist Analysis, Animation, and Application of Elastic Biomolecular Motion.The journal of physical chemistry. B · 2025Article
- Flexible fitting of AlphaFold2-predicted models to cryo-EM density maps using elastic network models: a methodical affirmation.Bioinformatics advances · 2025Article
- MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.Journal of chemical information and modeling · 2024Article
- Modeling and Simulation of the NMDA Receptor at Coarse-Grained and Atomistic Levels.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Predicting Protein Functional Motions: an Old Recipe with a New Twist.Biophysical journal · 2020Article
- Computational Ways to Enhance Protein Inhibitor Design.Frontiers in molecular biosciences · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Cryo_fit: Democratization of flexible fitting for cryo-EM.Journal of structural biology · 2019Article
- Normal Mode Analysis as a Routine Part of a Structural Investigation.Molecules (Basel, Switzerland) · 2019Review
- Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.Structure (London, England : 1993) · 2019Article
- Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics.BMC structural biology · 2018Article
- Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy.Biophysical journal · 2018Article
- Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling.Proteins · 2017Article
- Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.Biophysical journal · 2017Article
- Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling.Biophysical journal · 2017Article
- Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations.Scientific reports · 2016Article
- Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes.Biochimica et biophysica acta · 2014Review
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1 author.
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Abstract
Cryo-electron microscopy (cryo-EM) has been widely used to explore conformational states of large biomolecular assemblies. The detailed interpretation of cryo-EM data requires the flexible fitting of a known high-resolution protein structure into a low-resolution cryo-EM map. To this end, we have developed what we believe is a new method based on a two-bead-per-residue protein representation, and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method minimizes a pseudo-energy which linearly combines various terms of the modified elastic network model energy with a cryo-EM-fitting score and a collision energy that penalizes steric collisions. Unlike previous flexible fitting efforts using the lowest few normal modes, our method effectively utilizes all normal modes so that both global and local structural changes can be fully modeled. We have validated our method for a diverse set of 10 pairs of protein structures using simulated cryo-EM maps with a range of resolutions and in the absence/presence of random noise. We have shown that our method is both accurate and efficient compared with alternative techniques, and its performance is robust to the addition of random noise. Our method is also shown to be useful for the flexible fitting of three experimental cryo-EM maps.
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