The Protein Folding and Aggregation Simulator
PROFASI (PROtein Folding and Aggregation SImulator [1]) is a C++ program package for Monte Carlo simulations of protein folding and aggregation. It provides an implementation of an all-atom protein model with fixed bond lengths and bond angles, an implicit water simplified force field, and a set of tools to perform Monte Carlo simulations with the model. PROFASI version 2 introduces a plugins based extensible framework for Markov Chain Monte Carlo simulations involving proteins.
Contents:
- Introduction
- Brief change log for PROFASI version 2.0
- Installation instructions for ProFASi version 2.1
- Tutorials
- ProFASi executables
- BasicMCRun program reference
- SimTempRun program reference
- SimAnnealRun program reference
- Parallel tempering with PROFASI
- Wang-Landau method with WLRun
- Regularization: approximating a protein structure
- A program to regularize PDB structures
- Usage [generate_contact_file]
- Minimize an expression over degrees of freedom of a protein molecule
- Usage [prf_runinfo]
- Usage [jtf_extract]
- Usage [jtf_split]
- Extracting a snapshot configuration
- Calculating run-time properties from traj files
- Usage [his1dexport]
- Usage [export_residuewise_props]
- Usage [mc_stats]
- Converting between structure file formats
- Usage [mc_stats]
- Usage [StAn]
- Calculating energies of a PROFASI generated PDB/XML file
- Usage [contact_order]
- MimiqA : A swiss army knife for RMSD calculations
- Shift periodic box in a ProFASi multi-chain pdb file
- Extracting parts of a PDB file
- Usage [prfxml]
- Creating PROFASI style histograms with prf_his1d
- PROFASI trajectory files
- API
Miscellaneous topics
- Initial structures in PROFASI simulations
- PROFASI’s XML structure file format
- ProFASi PDB handling: Selections and Filters
- Commands to set up the population
- Accepted sequence input format in PROFASI
- Commands for setting up measurements/Observables
- Commands for the Monte Carlo
- Commands for the random number generator
- Options for multi-temperature simulations
- Restraining simulations with a torsional angle potential
- Simulations with distance restraints
- Observables
- Conversion factors between PROFASI units and standard units
- Generating native contact lists
- Exporting ProFASi histograms with his1dexport
- Converting and ProFASi histograms with his1dconvert
- Merging binary data from His2D objects
- Querry plugins registered with the PROFASI build
- XML templates: Auto-generate complex XML nodes from tabular data