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Welcome to the ProtoSyn.jl documentation!

ProtoSyn.jl is a platform for molecular manipulation and simulation, with an emphasis on peptide design.

The main goal of ProtoSyn is to be a basis on top of which new tools and protocols can be experimented and prototyped. Taking advantage of Julia’s environment, ProtoSyn has been built with emergent technologies in mind, such as distributed computing, GPU and SIMD acceleration and machine learning models usage.

Features

  • Edit a peptide structure by removing, adding and mutating any number of residues
  • Create peptides from scratch by providing the desired sequence
  • Copy parts of other molecules and graft them together to create something new
  • Explore Ramachandran maps to introduce secondary structure variations
  • Run Monte Carlo simulations to optimize a structure or a sequence
  • Calculate energies and forces using native potentials (such as SASA/GB, Coulomb or simple harmonics) or commonly used tools now integrated in Julia (such as TorchANI or REF15 from PyRosetta).
  • Perform Steepest Descent optimizations
  • Explore rotamer libraries to optimize sidechain packaging
  • Select residues based on name, index, distance and other parameters, with a rich combinatory selection syntax
  • Perform rigid body docking of ligands
  • Include ramified carbohydrates and glycoproteins in your simulations, with support for sugar residues
  • Include non-canonical aminoacids (NCAAs) and post-translational modifications, such as methylation or phosporylation
  • Generate functionalized carbon models, including multi-layer & pore generation support

Getting started

Publications

A scientific paper about ProtoSyn.jl package is being written and should be available soon.

Contacts

jose.manuel.pereira@ua.pt

Acknowledgments

Acknowledgments

This work was developed within the scope of the project CICECO-Aveiro Institute of Materials, UIDB/50011/2020 & UIDP/50011/2020, financed by national funds through the Portuguese Foundation for Science and Technology/MCTES. José Pereira further acknowledges FCT financial support on the scope of the PhD scholarship SFRH/BD/138820/2018.