What is ProtoSyn.jl?
What is ProtoSyn.jl?
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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.
ProtoSyn's development was based on two main ideas:
Simplicity at it's core, modularity before performance.
If you can imagine it, you should be able to simulate it.
# Protein-folding-prediction
# Peptide-design
# Sidechain-packaging
# Custom-energy-functions
# Atomic-selection
# Energy-minimization
# Molecular-structural-modifications
# Conformational-exploration
Features
Features
Custom energy functions
Custom energy functions
Pick and choose individual components from a rich library of potentials & machine learning models to create an energy function specifically suited for the task at hands
Add custom energy components
Add custom energy components
Define and use custom energy components based on physical or statistical methods
Complex simulation algorithms
Complex simulation algorithms
Choose from an expansive list of simulation algorithms: Monte Carlo, ILS, Steepest Descent, among other; or create your own custom driver for the simulation
Rich selection syntax
Rich selection syntax
Apply modifications to specific regions with a rich selection syntax: use logical operators to join selections and specify with precision the target atoms
Efficient coordinate system
Efficient coordinate system
Employ manipulations and simulations using both cartesian and internal coordinate systems with an emphasis on performance of rotations & translations
Complete molecular manipulation suite
Complete molecular manipulation suite
Remove, add and mutate residues; remove and add sidechains; cut and paste whole molecules - ProtoSyn allows complete manipulation of a molecular system
Explore rotamer libraries
Explore rotamer libraries
Load, create & modify rotamers libraries: perform sidechain packaging algorithms
Experimental features
Experimental features
Explore experimental support for sugars and glycoproteins, as well as initial tests on Molecular Dynamics Drivers, among others.
Colaborate
Colaborate
ProtoSyn.jl is an open-source project. New contributions are always welcome and help ProtoSyn grow to its full potential. Find more information on the project's GitHub page and read the documentation for more details on the inner workings of the code.
ProtoSyn was developed by José Pereira & Sérgio M. Santos, CICECO & Departamento de Química, Universidade de Aveiro, Portugal. 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.
Contacts
Contacts
If you'd like to know more, please contact:
jose.manuel.pereira@ua.pt
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