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MESMER: minimal ensemble solutions to multiple experimental restraints.

Elihu C Ihms¹, Mark P Foster²

¹Ohio State University Biophysics Program, Department of Chemistry and Biochemistry, and Center for RNA Biology, The Ohio State University, Columbus, OH, USA Ohio State University Biophysics Program, Department of Chemistry and Biochemistry, and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.

Bioinformatics (Oxford, England)

|February 13, 2015

Summary

This summary is machine-generated.

Analyzing macromolecular structures requires understanding their dynamic nature. MESMER software helps researchers analyze conformational heterogeneity by refining structural ensembles against experimental data.

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Area of Science:

Structural biology
Computational biophysics

Background:

Macromolecular structures exhibit inherent heterogeneity and dynamic configurations, complicating bulk experimental analysis.
Ensemble-based approaches are crucial for quantitative insights into heterogeneous biological systems.
Simultaneous fitting of orthogonal structural data probes the range and population of accessible macromolecular structures.

Purpose of the Study:

To develop user-friendly software for analyzing macromolecular conformational heterogeneity.
To enable the identification of structural ensembles that recapitulate experimental data.
To provide a platform for integrating diverse quantitative experimental data types.

Main Methods:

Developed MESMER (Macromolecular Ensemble Modeling, Simulation, and Estimation of Refinement) software.
Utilized an ensemble-based approach comparing predicted data from structural collections to experimental results.
Incorporated a graphical user interface (GUI) and modular Python plugins for data computation and fitting.

Main Results:

MESMER software was developed to identify structural ensembles matching experimental data.
The software refines thousands of component structures from an input pool.
MESMER was successfully applied to analyze conformational heterogeneity in three distinct macromolecular systems.

Conclusions:

MESMER provides a streamlined and user-friendly solution for analyzing macromolecular conformational heterogeneity.
The software facilitates the quantitative study of dynamic and heterogeneous biological structures.
MESMER's modular design allows for broad applicability across various experimental data types.