easyAmber: a step away from inefficient ”static” approaches towards a deeper understanding of protein dynamics

Dmitry Suplatov¹, Yana Sharapova², Vytas Е vedas^3
1Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia, d.a.suplatov@belozersky.msu.ru
²Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia, sharapova@belozersky.msu.ru
³Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, vytas@belozersky.msu.ru

Molecular dynamics (MD) can improve the success rate of in silico tools for drug discovery and protein engineering by accounting for protein structure flexibility/plasticity and predicting the time-dependent behavior of a molecular system, but requires specialized training and skills, what impedes practical use by many investigators. We have developed easyAmber – a comprehensive toolbox to automate the MD routines implemented in the Amber package, freely available at https://biokinet.belozersky.msu.ru/easyAmber.