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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.