scholarly journals Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps

2021 ◽  
Author(s):  
Takaharu Mori ◽  
Genki Terashi ◽  
Daisuke Matsuoka ◽  
Daisuke Kihara ◽  
Yuji Sugita
Keyword(s):  
De Novo ◽  
Structure Modeling ◽  
Density Maps ◽  
Automatic Error

scholarly journals Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 82 ◽  
Author(s):  
Eman Alnabati ◽  
Daisuke Kihara
Keyword(s):  
Electron Microscopy ◽  
De Novo ◽  
Molecular Structures ◽  
Structure Modeling ◽  
Rapid Progress ◽  
Macromolecular Complexes ◽  
Modeling Methods ◽  
Cryo Electron Microscopy ◽  
Density Maps

Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure determination of macromolecular complexes. For modeling molecular structures from density maps of different resolutions, many algorithms have been developed. These algorithms can be categorized into rigid fitting, flexible fitting, and de novo modeling methods. It is also observed that machine learning (ML) techniques have been increasingly applied following the rapid progress of the ML field. Here, we review these different categories of macromolecule structure modeling methods and discuss their advances over time.

scholarly journals DeepTracer: Fast Cryo-EM Protein Structure Modeling and Special Studies on CoV-related Complexes

2020 ◽  
Author(s):  
Jonas Pfab ◽  
Nhut Minh Phan ◽  
Dong Si
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Structural Information ◽  
Protein Complexes ◽  
Complex Structure ◽  
Structure Modeling ◽  
Density Maps ◽  
Average Residue ◽  
Development Processes ◽  
Special Studies

AbstractInformation about macromolecular structure of protein complexes such as SARS-CoV-2, and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automatic deep learning-based method for fast de novo multi-chain protein complex structure determination from high-resolution cryo-electron microscopy (cryo-EM) density maps. We applied DeepTracer on a previously published set of 476 raw experimental density maps and compared the results with a current state of the art method. The residue coverage increased by over 30% using DeepTracer and the RMSD value improved from 1.29Å to 1.18Å. Additionally, we applied DeepTracer on a set of 62 coronavirus-related density maps, among them 10 with no deposited structure available in EMDataResource. We observed an average residue match of 84% with the deposited structures and an average RMSD of 0.93Å. Additional tests with related methods further exemplify DeepTracer’s competitive accuracy and efficiency of structure modeling. DeepTracer allows for exceptionally fast computations, making it possible to trace around 60,000 residues in 350 chains within only two hours. The web service is globally accessible at https://deeptracer.uw.edu.

scholarly journals De Novo Computational Protein Tertiary Structure Modeling Pipeline for Cryo-EM Maps of Intermediate Resolution

2020 ◽  
Vol 118 (3) ◽  
pp. 292a
Author(s):  
Daisuke Kihara ◽  
Genki Terashi ◽  
Sai Raghavendra Maddhuri Venkata Subramaniya
Keyword(s):  
Tertiary Structure ◽  
De Novo ◽  
Structure Modeling ◽  
Protein Tertiary Structure

scholarly journals A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps

2020 ◽  
Vol 432 (19) ◽  
pp. 5365-5377 ◽  
Author(s):  
Biao Zhang ◽  
Xi Zhang ◽  
Robin Pearce ◽  
Hong-Bin Shen ◽  
Yang Zhang
Keyword(s):  
Protein Structure ◽  
Atomic Level ◽  
Structure Modeling ◽  
Protein Structure Modeling ◽  
Density Maps ◽  
Medium Resolution

scholarly journals EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps

Structure ◽  
2012 ◽  
Vol 20 (3) ◽  
pp. 464-478 ◽  
Author(s):  
Steffen Lindert ◽  
Nathan Alexander ◽  
Nils Wötzel ◽  
Mert Karakaş ◽  
Phoebe L. Stewart ◽  
...  
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
De Novo ◽  
Protein Structure Determination ◽  
Density Maps ◽  
Medium Resolution

Exploring alternate states and oligomerization preferences of coiled-coils by de novo structure modeling

2014 ◽  
Vol 83 (2) ◽  
pp. 235-247 ◽  
Author(s):  
Sebastian Rämisch ◽  
Robert Lizatović ◽  
Ingemar André
Keyword(s):  
De Novo ◽  
Coiled Coils ◽  
Structure Modeling ◽  
Alternate States
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