Fast large-scale clustering of protein structures using Gauss integrals

Tim Philipp Harder; Mikael Borg; Wouter Krogh Boomsma; Peter Røgen; Thomas Wim Hamelryck

doi:10.1093/bioinformatics/btr692

Fast large-scale clustering of protein structures using Gauss integrals

Tim Philipp Harder, Mikael Borg, Wouter Krogh Boomsma, Peter Røgen, Thomas Wim Hamelryck

Computational and RNA Biology

21 Citations (Scopus)

Abstract

Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors-which were introduced by Røgen and co-workers-and subsequently performing K-means clustering. Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50 000 structures, can be clustered within seconds to minutes.

Original language	English
Journal	Bioinformatics
Volume	28
Issue number	4
Pages (from-to)	510-515
Number of pages	6
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btr692
Publication status	Published - Feb 2012

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title = "Fast large-scale clustering of protein structures using Gauss integrals",

abstract = "Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors-which were introduced by R{\o}gen and co-workers-and subsequently performing K-means clustering. Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50 000 structures, can be clustered within seconds to minutes.",

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T1 - Fast large-scale clustering of protein structures using Gauss integrals

AU - Harder, Tim Philipp

AU - Borg, Mikael

AU - Boomsma, Wouter Krogh

AU - Røgen, Peter

AU - Hamelryck, Thomas Wim

PY - 2012/2

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N2 - Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors-which were introduced by Røgen and co-workers-and subsequently performing K-means clustering. Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50 000 structures, can be clustered within seconds to minutes.

AB - Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors-which were introduced by Røgen and co-workers-and subsequently performing K-means clustering. Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50 000 structures, can be clustered within seconds to minutes.

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Fast large-scale clustering of protein structures using Gauss integrals

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