MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics

The term clustering designates a comprehensive family of unsupervised learning methods allowing to group similar elements into sets called clusters. Geometrical clustering of molecular dynamics (MD) trajectories is a well-established analysis to gain insights into the conformational behavior of simu...

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Published in:Bioinformatics (Oxford, England) Vol. 38; no. 23; pp. 5191 - 5198
Main Authors: González-Alemán, Roy, Platero-Rochart, Daniel, Rodríguez-Serradet, Alejandro, Hernández-Rodríguez, Erix W, Caballero, Julio, Leclerc, Fabrice, Montero-Cabrera, Luis
Format: Journal Article
Language:English
Published: England Oxford University Press (OUP) 30.11.2022
Subjects:
Algorithms
Biochemistry, Molecular Biology
Biophysics
Chemical Sciences
Cluster Analysis
Life Sciences
Molecular Dynamics Simulation
or physical chemistry
Software
Theoretical and
ISSN:1367-4803, 1367-4811, 1367-4811
Online Access:Get full text
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Summary:The term clustering designates a comprehensive family of unsupervised learning methods allowing to group similar elements into sets called clusters. Geometrical clustering of molecular dynamics (MD) trajectories is a well-established analysis to gain insights into the conformational behavior of simulated systems. However, popular variants collapse when processing relatively long trajectories because of their quadratic memory or time complexity. From the arsenal of clustering algorithms, HDBSCAN stands out as a hierarchical density-based alternative that provides robust differentiation of intimately related elements from noise data. Although a very efficient implementation of this algorithm is available for programming-skilled users (HDBSCAN*), it cannot treat long trajectories under the de facto molecular similarity metric RMSD. Here, we propose MDSCAN, an HDBSCAN-inspired software specifically conceived for non-programmers users to perform memory-efficient RMSD-based clustering of long MD trajectories. Methodological improvements over the original version include the encoding of trajectories as a particular class of vantage-point tree (decreasing time complexity), and a dual-heap approach to construct a quasi-minimum spanning tree (reducing memory complexity). MDSCAN was able to process a trajectory of 1 million frames using the RMSD metric in about 21 h with <8 GB of RAM, a task that would have taken a similar time but more than 32 TB of RAM with the accelerated HDBSCAN* implementation generally used. The source code and documentation of MDSCAN are free and publicly available on GitHub (https://github.com/LQCT/MDScan.git) and as a PyPI package (https://pypi.org/project/mdscan/). Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btac666