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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.

John E Stone¹, Ryan McGreevy, Barry Isralewitz

¹Beckman Institute, University of Illinois, 405 N. Mathews Ave, Urbana, IL, USA.

Faraday Discussions

|October 24, 2014

Summary

New algorithms accelerate the analysis of large biomolecular structures by combining cryo-electron microscopy and X-ray crystallography data with molecular dynamics simulations. This enables faster quality-of-fit evaluation for complex biological systems.

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Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Hybrid structure fitting methods integrate cryo-electron microscopy (cryo-EM) and X-ray crystallography data with molecular dynamics (MD) simulations.
Accurate determination of all-atom structures for large biomolecular complexes is crucial for understanding their function.
Evaluating the quality-of-fit in these hybrid methods is computationally intensive, especially for large complexes and long MD trajectories.

Purpose of the Study:

To develop and present novel data-parallel and GPU-accelerated algorithms for rapid, interactive computation of quality-of-fit metrics.
To enable efficient analysis of large biomolecular complexes and long MD trajectories in hybrid structure fitting.
To improve the visualization of results from hybrid structure fitting methods.

Main Methods:

Development of data-parallel and GPU-accelerated algorithms for quality-of-fit metric computation.
Integration of algorithms with cryo-EM and X-ray crystallography density maps and all-atom structures.
Application to molecular dynamics trajectories for large biomolecular complexes.

Main Results:

The new algorithms provide rapid and interactive computation of quality-of-fit metrics.
Performance and accuracy of the new algorithms were evaluated against existing tools.
Algorithm performance was assessed on both GPU-accelerated workstations and supercomputers.
New visualization techniques for hybrid structure fitting results were described.

Conclusions:

The developed algorithms significantly enhance the speed and interactivity of quality-of-fit analysis for large biomolecular structures.
These advancements facilitate the study of complex systems like viruses and protein folding.
The methods improve the integration of experimental data with computational simulations for structural biology.