Cargando…

Detecting protein and DNA/RNA structures in cryo-EM maps of intermediate resolution using deep learning

An increasing number of density maps of macromolecular structures, including proteins and DNA/RNA complexes, have been determined by cryo-electron microscopy (cryo-EM). Although lately maps at a near-atomic resolution are routinely reported, there are still substantial fractions of maps determined a...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wang, Xiao, Alnabati, Eman, Aderinwale, Tunde W., Maddhuri Venkata Subramaniya, Sai Raghavendra, Terashi, Genki, Kihara, Daisuke
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2021
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052361/ https://www.ncbi.nlm.nih.gov/pubmed/33863902 http://dx.doi.org/10.1038/s41467-021-22577-3

Ejemplares similares

Protein Secondary Structure Detection in Intermediate Resolution Cryo-EM Maps Using Deep Learning
por: Subramaniya, Sai Raghavendra Maddhuri Venkata, et al.
Publicado: (2019)

Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling
por: Maddhuri Venkata Subramaniya, Sai Raghavendra, et al.
Publicado: (2023)

Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction
por: Jain, Aashish, et al.
Publicado: (2021)

Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST
por: Alnabati, Eman, et al.
Publicado: (2022)

Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps
por: Alnabati, Eman, et al.
Publicado: (2019)

Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score
por: Terashi, Genki, et al.
Publicado: (2023)

MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field
por: Alnabati, Eman, et al.
Publicado: (2022)

VESPER: global and local cryo-EM map alignment using local density vectors
por: Han, Xusi, et al.
Publicado: (2021)

Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps
por: Mori, Takaharu, et al.
Publicado: (2021)

De novo main-chain modeling for EM maps using MAINMAST
por: Terashi, Genki, et al.
Publicado: (2018)

Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly
por: He, Jiahua, et al.
Publicado: (2022)

The Local Resolution of Cryo-EM Density Maps
por: Kucukelbir, Alp, et al.
Publicado: (2013)

Real-time structure search and structure classification for AlphaFold protein models
por: Aderinwale, Tunde, et al.
Publicado: (2022)

De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge
por: Terashi, Genki, et al.
Publicado: (2018)

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies
por: Dror, Oranit, et al.
Publicado: (2007)

AlphaFold2 and CryoEM: Revisiting CryoEM modeling in near-atomic resolution density maps
por: Hryc, Corey F., et al.
Publicado: (2022)

RL-MLZerD: Multimeric protein docking using reinforcement learning
por: Aderinwale, Tunde, et al.
Publicado: (2022)

Automatic local resolution-based sharpening of cryo-EM maps
por: Ramírez-Aportela, Erney, et al.
Publicado: (2019)

Primed for Discovery: Atomic-Resolution Cryo-EM Structure of a Reovirus Entry Intermediate
por: Trask, Shane D., et al.
Publicado: (2010)

Interpreting the cryo-EM map
por: Rosenthal, Peter B.
Publicado: (2019)

Measuring local-directional resolution and local anisotropy in cryo-EM maps
por: Vilas, Jose Luis, et al.
Publicado: (2020)

Interpretation of medium resolution cryoEM maps of multi-protein complexes
por: Casañal, Ana, et al.
Publicado: (2019)

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps
por: Si, Dong, et al.
Publicado: (2020)

Density modification of cryo-EM maps
por: Terwilliger, Thomas C., et al.
Publicado: (2020)

The cryo-EM resolution revolution and transcription complexes
por: Hanske, Jonas, et al.
Publicado: (2018)

Single-particle cryo-EM: beyond the resolution
por: Armache, Jean-Paul, et al.
Publicado: (2019)

Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model
por: Kim, Doo Nam, et al.
Publicado: (2017)

Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ
por: Chen, Siyu, et al.
Publicado: (2023)

Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution
por: Kulik, Marta, et al.
Publicado: (2021)

Confidence maps: statistical inference of cryo-EM maps
por: Beckers, Maximilian, et al.
Publicado: (2020)

Improvement of cryo-EM maps by simultaneous local and non-local deep learning
por: He, Jiahua, et al.
Publicado: (2023)

Improvement of cryo-EM maps by density modification
por: Terwilliger, Thomas C., et al.
Publicado: (2020)

De novo protein structure determination from near-atomic resolution cryo-EM maps
por: Wang, Ray Yu-Ruei, et al.
Publicado: (2015)

EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps
por: He, Jiahua, et al.
Publicado: (2021)

Topaz-Denoise: general deep denoising models for cryoEM and cryoET
por: Bepler, Tristan, et al.
Publicado: (2020)

Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps
por: Habeck, Michael
Publicado: (2017)

Likelihood-based docking of models into cryo-EM maps
por: Millán, Claudia, et al.
Publicado: (2023)

High-resolution cryo-EM proteasome structures in drug development
por: Morris, Edward P., et al.
Publicado: (2017)

High-resolution cryo-EM reconstructions in the presence of substantial aberrations
por: Bromberg, Raquel, et al.
Publicado: (2020)

Model-based local density sharpening of cryo-EM maps
por: Jakobi, Arjen J, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_937bngc3fhrocs4dicqts76a07