MDaRes: MD Analysis of Residue Properties Using Structural Alphabets

Analyze molecular dynamics (MD) simulation data using structural alphabets. Protein local conformations from molecular simulations are encoded in a compressed string representation. Residue-level UniProt annotations can be directly retrieved. Comparative analysis tools are available to investigate conformational variability, coordinated motions, and differences between systems (e.g. wild-type vs mutant; bound vs unbound). Methodological details for the structural alphabet analysis can be found in Pandini et al. (2013) <doi:10.1093/bioinformatics/btt326>.

Version:	0.0.2
Depends:	R (≥ 4.1.0)
Imports:	bio3d, DescTools, SOMMD, tools, dplyr, tidyr, stringr, UniprotR, Rcpp
LinkingTo:	Rcpp, RcppArmadillo
Suggests:	httr, future, future.apply, curl, testthat (≥ 3.0.0)
Published:	2026-08-25
DOI:	10.32614/CRAN.package.MDaRes (may not be active yet)
Author:	Nancy D'Arminio [aut], Anna Marabotti [aut], Alessandro Pandini [aut, cph, cre]
Maintainer:	Alessandro Pandini <alessandro.pandini at gmail.com>
License:	GPL-3
NeedsCompilation:	yes
Materials:	README, NEWS
CRAN checks:	MDaRes results

Documentation:

Reference manual:

MDaRes.html , MDaRes.pdf

Downloads:

Package source:	MDaRes_0.0.2.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: MDaRes_0.0.2.zip
macOS binaries:	r-release (arm64): MDaRes_0.0.2.tgz, r-oldrel (arm64): MDaRes_0.0.2.tgz, r-release (x86_64): MDaRes_0.0.2.tgz, r-oldrel (x86_64): MDaRes_0.0.2.tgz

Linking:

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