De Novo Main-chain Modeling for EM Maps Using MAINMAST

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Apr 26

PMID 29691408

Citations 58

Authors

Genki Terashi

Daisuke Kihara

Affiliations

Soon will be listed here.

Abstract

An increasing number of protein structures are determined by cryo-electron microscopy (cryo-EM) at near atomic resolution. However, tracing the main-chains and building full-atom models from EM maps of ~4-5 Å is still not trivial and remains a time-consuming task. Here, we introduce a fully automated de novo structure modeling method, MAINMAST, which builds three-dimensional models of a protein from a near-atomic resolution EM map. The method directly traces the protein's main-chain and identifies Cα positions as tree-graph structures in the EM map. MAINMAST performs significantly better than existing software in building global protein structure models on data sets of 40 simulated density maps at 5 Å resolution and 30 experimentally determined maps at 2.6-4.8 Å resolution. In another benchmark of building missing fragments in protein models for EM maps, MAINMAST builds fragments of 11-161 residues long with an average RMSD of 2.68 Å.

Citing Articles

AI-based methods for biomolecular structure modeling for Cryo-EM.

Farheen F, Terashi G, Zhu H, Kihara D Curr Opin Struct Biol. 2025; 90:102989.

PMID: 39864242 PMC: 11793015. DOI: 10.1016/j.sbi.2025.102989.

Secondary Structure Detection and Structure Modeling for Cryo-EM.

Punuru P, Jain A, Kihara D Methods Mol Biol. 2024; 2870:341-355.

PMID: 39543043 DOI: 10.1007/978-1-0716-4213-9_17.

Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.

Li T, Cao H, He J, Huang S Nat Commun. 2024; 15(1):9367.

PMID: 39477926 PMC: 11525807. DOI: 10.1038/s41467-024-53721-4.

DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model.

Wang X, Zhu H, Terashi G, Taluja M, Kihara D Nat Methods. 2024; 21(12):2307-2317.

PMID: 39433880 DOI: 10.1038/s41592-024-02479-0.

CryoTEN: Efficiently Enhancing Cryo-EM Density Maps Using Transformers.

Selvaraj J, Wang L, Cheng J bioRxiv. 2024; .

PMID: 39314387 PMC: 11418965. DOI: 10.1101/2024.09.06.611715.

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