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Updated: Mar 8, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Protein structure determination using metagenome sequence data.

Sergey Ovchinnikov^1,2,3, Hahnbeom Park^1,2, Neha Varghese⁴

¹Department of Biochemistry, University of Washington, Seattle, WA 98105, USA.

Science (New York, N.Y.)

|January 21, 2017

Summary

This summary is machine-generated.

Researchers accurately modeled unknown protein structures using evolutionary data and metagenome sequences. This cost-effective approach expands the Protein Data Bank and aids protein structure initiative goals.

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Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Thousands of protein families lack known structures, hindering biological research.
Current methods like comparative modeling are insufficient for many proteins.

Purpose of the Study:

To develop and validate a computational approach for predicting protein structures.
To expand the number of protein families with available structural models.

Main Methods:

Utilized Rosetta structure prediction guided by evolutionary residue-residue contacts.
Integrated metagenome sequence data to increase the pool of modelable protein families.
Employed contact-based structure matching and Rosetta calculations for model generation.

Main Results:

Accurately modeled proteins within large families using evolutionary information.
Metagenome data tripled the number of protein families suitable for accurate modeling.
Generated models for 614 previously uncharacterized protein families, including membrane proteins and novel folds.

Conclusions:

The combined approach significantly advances protein structure prediction capabilities.
This method provides cost-effective representative models for large protein families.
The study contributes valuable structural data for underrepresented protein families.