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Updated: Dec 14, 2025

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.
Abstract:
We present a highly parallel algorithm to convert internal coordinates of a polymeric molecule into Cartesian coordinates. Traditionally, converting the structures of polymers (e.g., proteins) from internal to Cartesian coordinates has been performed serially, due to an inherent linear dependency along the polymer chain. We show this dependency can be removed using a tree-based concatenation of coordinate transforms between segments, and then parallelized efficiently on graphics processing units (GPUs). The conversion algorithm is applicable to protein engineering and fitting protein structures to experimental data, and we observe an order of magnitude speedup using parallel processing on a GPU compared to serial execution on a CPU.
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