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bioRxiv · 10.1101/2023.08.21.554196

DSSP in Gromacs: tool for defining secondary structures of proteins in trajectories

Gorelov, S. V.·Titov, A. I.·Shvetsov, A. V.
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Abstract

This work describes a fast implementation of software algorithm associated with determination of protein secondary structure based on the DSSP algorithm. This implementation is fully compatible with the DSSP v.4 algorithm and implemented as native Gromacs trajectory analysis module which allows to analyze molecular dynamics trajectories without any restrictions of the original DSSP implementation. Also this implementation works much faster then original DSSP v.4 algorithm. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/554196v3_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@190b391org.highwire.dtl.DTLVardef@fcf564org.highwire.dtl.DTLVardef@1529a97org.highwire.dtl.DTLVardef@236793_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Gorelov, S. V., Titov, A. I., Shvetsov, A. V.. 2023-08-25. DSSP in Gromacs: tool for defining secondary structures of proteins in trajectories. https://doi.org/10.1101/2023.08.21.554196

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