PROFASI: The Protein Folding and Aggregation Simulator

Principal Investigator: 

Sandipan Mohanty
Jülich Supercomputing Centre
Email: s.mohanty@fz-juelich.de

Other application users/developers: 

Main collaborator in PROFASI development:
Anders Irbäck, Lund University, Sweden

Scientific area: 
Computational Biophysics
Abstract: 
PROFASI is a Monte Carlo simulation package for protein folding and aggregation simulations written in C++ (now, partially C++11). It implements an all-atom protein model, an implicit solvent interaction potential and several modern Monte Carlo methods for simulation of systems with rough energy landscapes. It has been used to study folding and thermodynamics of helical, beta sheet and mixed proteins of up to 92 amino acids. It has also been used to study the aggregation of disease related peptides from 6 to 140 amino acids and the thermal/mechanical unfolding of many proteins.
Scalability: 
Weak scaling to 16384 cores on BGP and 4096 cores on x86_64 based clusters.
Versions: 
MPI
Other: 
C++11 threads / pthreads
Tested on platforms: 

x86/ARM based clusters, BG/P, BG/Q

Images: 
Any other information: 

As of April 2013, Top7 is the largest and most complex protein folded with an all-atom protein model using unconstrained physical simulations from random initial conformations. This simulation was done with PROFASI.  (http://onlinelibrary.wiley.com/doi/10.1002/prot.24295/pdf)