PHAST: Protein-like heteropolymer analysis by statistical thermodynamics

Abstract

PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data can be straightforwardly analyzed within its microcanonical Statistical Thermodynamics module, which allows for computing the entropy, caloric curve, specific heat and free energies. As a case study, we investigate the aggregation of heteropolymers bioinspired on $A{\beta }_{25-33}$ fragments and their cross-seeding with $IAP{P}_{20-29}$ isoforms. Excellent parallel scaling is observed, even under numerically difficult first-order like phase transitions, which are properly described by the built-in fully reconfigurable force fields. Still, the package is free and open source, this shall motivate users to readily adapt it to specific purposes.

18 pages, 8 figures, accepted by Comp. Phys. Commun. Related software application, PHAST, registered under GPL v3 license

References in corpus (6)

• Microcanonical Analyses of Peptide Aggregation Processes
• Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin
• Microcanonical versus Canonical Analysis of Protein Folding
• Aggregation of theta-polymers in spherical confinement
• Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity
• Breakout character of islet amyloid polypeptide hydrophobic mutations at the onset of type-2 diabetes