AlphaFold2-RAVE: From Sequence to Boltzmann Ranking
Bodhi P. Vani, Akashnathan Aranganathan, Dedi Wang, Pratyush Tiwary
Abstract
While AlphaFold2 is rapidly being adopted as a new standard in protein structure predictions, it is limited to single structures. This can be insufficient for the inherently dynamic world of biomolecules. In this Letter, we propose AlphaFold2-RAVE, an efficient protocol for obtaining Boltzmann-ranked ensembles from sequence. The method uses structural outputs from AlphaFold2 as initializations for artificial intelligence-augmented molecular dynamics. We release the method as an open-source code and demonstrate results on different proteins.
Topics & Concepts
Sequence (biology)Computer scienceRanking (information retrieval)Code (set theory)Protocol (science)Artificial intelligenceData miningBiologyGeneticsSet (abstract data type)Alternative medicinePathologyMedicineProgramming languageProtein Structure and DynamicsRNA and protein synthesis mechanismsMachine Learning in Bioinformatics