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Frank DiMaio
Frank DiMaio
Verified email at uw.edu
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Year
Accurate prediction of protein structures and interactions using a three-track neural network
M Baek, F DiMaio, I Anishchenko, J Dauparas, S Ovchinnikov, GR Lee, ...
Science 373 (6557), 871-876, 2021
34552021
The Rosetta all-atom energy function for macromolecular modeling and design
RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ...
Journal of chemical theory and computation 13 (6), 3031-3048, 2017
12692017
High-resolution comparative modeling with RosettaCM
Y Song, F DiMaio, RYR Wang, D Kim, C Miles, TJ Brunette, J Thompson, ...
Structure 21 (10), 1735-1742, 2013
11362013
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
BA Barad, N Echols, RYR Wang, Y Cheng, F DiMaio, PD Adams, ...
Nature methods 12 (10), 943-946, 2015
7402015
Crystal structure of a monomeric retroviral protease solved by protein folding game players
F Khatib, F DiMaio, Foldit Contenders Group, Foldit Void Crushers Group, ...
Nature structural & molecular biology 18 (10), 1175-1177, 2011
6772011
Structure prediction for CASP8 with all‐atom refinement using Rosetta
S Raman, R Vernon, J Thompson, M Tyka, R Sadreyev, J Pei, D Kim, ...
Proteins: Structure, Function, and Bioinformatics 77 (S9), 89-99, 2009
5932009
Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
5802020
Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer
AC Walls, MA Tortorici, BJ Bosch, B Frenz, PJM Rottier, F DiMaio, FA Rey, ...
Nature 531 (7592), 114-117, 2016
5422016
Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules
H Park, P Bradley, P Greisen Jr, Y Liu, VK Mulligan, DE Kim, D Baker, ...
Journal of chemical theory and computation 12 (12), 6201-6212, 2016
4172016
De novo protein design by deep network hallucination
I Anishchenko, SJ Pellock, TM Chidyausiku, TA Ramelot, S Ovchinnikov, ...
Nature 600 (7889), 547-552, 2021
4152021
Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy
AC Walls, MA Tortorici, B Frenz, J Snijder, W Li, FA Rey, F DiMaio, ...
Nature structural & molecular biology 23 (10), 899-905, 2016
4002016
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
RYR Wang, Y Song, BA Barad, Y Cheng, JS Fraser, F DiMaio
Elife 5, e17219, 2016
3982016
Relaxation of backbone bond geometry improves protein energy landscape modeling
P Conway, MD Tyka, F DiMaio, DE Konerding, D Baker
Protein science 23 (1), 47-55, 2014
3702014
Alternate states of proteins revealed by detailed energy landscape mapping
MD Tyka, DA Keedy, I André, F DiMaio, Y Song, DC Richardson, ...
Journal of molecular biology 405 (2), 607-618, 2011
3612011
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
SE Boyken, Z Chen, B Groves, RA Langan, G Oberdorfer, A Ford, ...
Science 352 (6286), 680-687, 2016
3562016
Near-atomic model of microtubule-tau interactions
EH Kellogg, NMA Hejab, S Poepsel, KH Downing, F DiMaio, E Nogales
Science 360 (6394), 1242-1246, 2018
3442018
De novo design of protein structure and function with RFdiffusion
JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim, HE Eisenach, ...
Nature 620 (7976), 1089-1100, 2023
3392023
Atomic-accuracy models from 4.5-Ĺ cryo-electron microscopy data with density-guided iterative local refinement
F DiMaio, Y Song, X Li, MJ Brunner, C Xu, V Conticello, E Egelman, ...
Nature methods 12 (4), 361-365, 2015
3302015
Refinement of protein structures into low-resolution density maps using rosetta
F DiMaio, MD Tyka, ML Baker, W Chiu, D Baker
Journal of molecular biology 392 (1), 181-190, 2009
3202009
High thermodynamic stability of parametrically designed helical bundles
PS Huang, G Oberdorfer, C Xu, XY Pei, BL Nannenga, JM Rogers, ...
science 346 (6208), 481-485, 2014
3172014
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