MDaRes

Authors Nancy D'Arminio, Anna Marabotti, Alessandro Pandini

Last update 25 August 2026

Copyright license GNU General Public License, version 3.0

Description

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>.

Cites work

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet

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