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Related Experiment Video

Updated: Dec 14, 2025

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

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

Published on: July 16, 2017

High-performance transformation of protein structure representation from internal to Cartesian coordinates.

Mahsa Bayati¹, Miriam Leeser¹, Jaydeep P Bardhan²

¹Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts, USA.

Journal of Computational Chemistry

|July 21, 2020

Summary

We developed a parallel algorithm to convert polymer structures from internal to Cartesian coordinates, overcoming serial limitations. This GPU-accelerated method significantly speeds up calculations for protein engineering and structure fitting.

Keywords:

GPU computing HPC protein

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Published on: July 14, 2015

Area of Science:

Computational chemistry
Molecular modeling
Bioinformatics

Background:

Converting internal molecular coordinates to Cartesian coordinates is crucial for structural analysis.
Traditional methods are serial, creating a bottleneck for large polymeric molecules like proteins.

Purpose of the Study:

To develop a highly parallel algorithm for converting internal coordinates to Cartesian coordinates in polymeric molecules.
To overcome the inherent linear dependency that necessitates serial processing in traditional methods.

Main Methods:

A tree-based concatenation of coordinate transforms between molecular segments was employed.
The algorithm was parallelized efficiently on graphics processing units (GPUs).

Main Results:

The inherent linear dependency along the polymer chain was successfully removed.
An order of magnitude speedup was observed using parallel GPU processing compared to serial CPU execution.

Conclusions:

The presented parallel algorithm offers a significant computational advantage for molecular structure conversions.
This method is applicable to protein engineering and fitting protein structures to experimental data, enhancing efficiency.