[ANN] ProtoSyn.jl v1.1: Molecular manipulation and simulation

Hi everyone! I’m excited to officially share with you ProtoSyn.jl: a new tool for molecular simulation and general manipulation, with a strong emphasis on protein design. I’ve been showcasing ProtoSyn.jl for a while, but it seems fitting to make the classical announcement here as well.

The main goal of ProtoSyn.jl 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/SIMD acceleration and machine learning models usage. ProtoSyn.jl intends to be a playground for trying out new emergent models and algorithms in a plug-and-play environment, completly open-source and with curated & up-do-date documentation, examples and tutorials.

Some 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

Perhaps this is a more “especialized” package for the general Julia community, but, for anyone interested, I’m 100% happy, eager and ready to explain, comment and just chat about it! Thank you for your time!

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Protein design seems to be a rapidly growing and important field, and it is nice to see Julia being used within it - it is just an obvious match.

I think it is too late to sign up, but would you ever concider giving a talk about this in JuliaCon or similar events?

I’m actually going to give a flash talk on JuliaCON this year! Feel free to tune in and ask questions.
I always love to talk about this stuff.

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