picodase
Designing new enzymes with physical chemistry and machine learning
University of Washington, DiMaio labSeattle, WA
Pinned Repositories
avogadro
Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
bioicons
A library of free open source icons for science illustrations in biology and chemistry
cbpcode
cs271-final-project
cs446_final
Final project for Networks in Computational Biology at Oregon State University
dpgen
The deep potential generator
dynafeature
A library for featurizing protein dynamics data for molecular design.
mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
mdsimple
A command-line utility to easily create, setup, and submit a set of MD experiments to a job scheduler on a cluster. Initially supports GROMACS simulations and the PBS job scheduler.
SORETTA
Protein function prediction and protein unfolding package for computational protein design
picodase's Repositories
picodase/bioicons
A library of free open source icons for science illustrations in biology and chemistry
picodase/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
picodase/mdsimple
A command-line utility to easily create, setup, and submit a set of MD experiments to a job scheduler on a cluster. Initially supports GROMACS simulations and the PBS job scheduler.
picodase/SORETTA
Protein function prediction and protein unfolding package for computational protein design
picodase/avogadro
Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
picodase/cbpcode
picodase/cs271-final-project
picodase/cs446_final
Final project for Networks in Computational Biology at Oregon State University
picodase/dpgen
The deep potential generator
picodase/dynafeature
A library for featurizing protein dynamics data for molecular design.
picodase/Dynamics
Dynamics PyMOL Plugin
picodase/enlighten2-pymol
PyMOL plugin for enlighten2
picodase/enzymodel
Effort to comprehensively model enzymatic function as observed in the literature
picodase/getcontacts
Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation
picodase/GROMACS_Examples
Examples showing how to run GROMACS molecular dynamics simulations
picodase/mlplayground
Collection of prototype scripts for machine learning frameworks prior to a complete project repo idea formulation.
picodase/picodase
Config files for my GitHub profile.
picodase/picodase.github.io
My project demonstration site
picodase/PiViewer
PiViewer: an open-source tool for automated detection and display of pi-pi interactions
picodase/PlotNeuralNet
Latex code for making neural networks diagrams
picodase/PREFMoDeL
A library of features describing single molecules (especially proteins)
picodase/PyMine
A PyMOL plugin to integrate and visualize data for drug discovery
picodase/Pymol-script-repo
Collected scripts for Pymol
picodase/RIP-MD
picodase/spharmophore
Structure-based pharmacophore and ligand family generator.
picodase/stsophore
Transition-state feature-based enzyme scaffold family generator.
picodase/xcompose
for sharing .XCompose keybindings