F. Dimaio

Publications221
h-index50
Citations8,316
Highly Influential Citations437
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High-resolution comparative modeling with RosettaCM.
TLDR
We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures by recombining aligned segments in Cartesian space and building unaligned regions de novo. Expand
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to… Expand
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Structure prediction for CASP8 with all‐atom refinement using Rosetta
TLDR
We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Expand
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EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that… Expand
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Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This… Expand
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Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
TLDR
We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Expand
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Crystal structure of a monomeric retroviral protease solved by protein folding game players
Following the failure of a wide range of attempts to solve the crystal structure of M-PMV retroviral protease by molecular replacement, we challenged players of the protein folding game Foldit to… Expand
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Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local… Expand
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Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy
The threat of a major coronavirus pandemic urges the development of strategies to combat these pathogens. Human coronavirus NL63 (HCoV-NL63) is an α-coronavirus that can cause severe… Expand
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Near-atomic model of microtubule-tau interactions
Tackling microtubule-tau interactions Alzheimer's disease is a major cause of death in the elderly. Disease progression is associated with the accumulation of neurofibrillary tangles composed of tau,… Expand
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