XdynBP – molecular modeling core for hydbrid QM/MM simulations using the EVB framework

(as a courtesy of Dr Letif Mones)

 

PMFlib – library for free energy calculations, including methods: Umbrella Sampling, Constraint Dynamics (Blue Moon), Metadynamics, Adaptive Biasing Force, String Method

 

DisAlign – aligning proteins with intrinsically disordered regions