Poster (Outreach)

FZJ-2025-05842

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png All-Atom MCMC Simulation of Protein Folding with ProFASi

Zimmermann, O. (Corresponding author)FZJ* ; Meinke, J.FZJ* ; Mohanty, S.FZJ*

2025

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Please use a persistent id in citations: doi:10.34734/FZJ-2025-05842

Abstract: We will introduce ProFASi, a versatile open source software for simulation of biomolecular structure formation such as protein folding or peptide aggregation. An all-atom representation of the protein molecules with implicit solvent is used in ProFASi. The software features efficient implementations of several Monte Carlo methods that update the torsional degrees of freedom, as well as global translation and rotation of individual molecules. ProFASi has been used to perform unbiased simulations of protein folding of several small molecules including the designed 92 aa protein Top7 as well as simulation of peptide aggregation up to 512 hexapeptides. Several use cases and options for plugin development are presented.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)

Research Program(s):

1. 5111 - Domain-Specific Simulation & Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) (POF4-511)

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