akos-bio1's repositories
qProtein
A platform for structural proteomics analysis.
CodonTransformer
The ultimate tool for codon optimization, transforming protein sequences into optimized DNA sequences specific for your target organisms.
PocketGen
Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
computational-chemistry
Google Colaboratory Notebooks for Computational Biochemistry
GGAssembler
Create a cost sensitive degenerate codon sequence
nucleus
b.next nucleus open-source cell developer kit
mace
MACE - Fast and accurate machine learning interatomic potentials with higher order equivariant message passing.
DASH-tree
Partial Charge assignment for Molecular Dynamics
mdtraj
An open library for the analysis of molecular dynamics trajectories
ABFE_workflow
This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
polymerist
Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools
refit-espaloma
Refit espaloma with energies and forces
DynamicBind
repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
espfit-experiment
Workspace for espfit
WaSP_simulations
Repository for housing minimal reproducing scripts and chemical structures for water-soluble polymer (WaSP) MD studies
vanilla-espaloma-experiment
Vanilla MD simulation of protein-ligand complex using espaloma-0.3
polymer_examples
Example polymers for testing.
simple-simulate-complex
Simple protein-ligand complex simulation with OpenMM
2019_SDASD
Codes for ribosome profiling study of SD-ASD interaction
openmm-rna
a reimplementation of work by seetin et al. for RNA tertiary structure prediction