SallyS.'s starred repositories
pymol-color-alphafold
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
remd_temperature
Python library to query web server with temperature generator for REMD-simulations
torsional-diffusion
Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)
ScaffoldGraph
ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.
moleculekit
MoleculeKit: Your favorite molecule manipulation kit
DROIDS-2.0---free-software-for-comparative-protein-dynamics
DROIDS v2.0 final beta release is done. It now incorporates the ability to create and analyze mutant model dynamics. New pipelines for protein-ligand and DNA-protein interaction and multi-chain complexes are supported. IMPORTANT: DROIDS v3.0 is now available here https://github.com/gbabbitt/DROIDS-3.0-comparative-protein-dynamics
protein-ligand-benchmark
Protein-Ligand Benchmark Dataset for Free Energy Calculations
nbdev_template
Template for nbdev projects
De_novo_design_SARSCOV2
Notebooks and files from the paper De novo Design and Bioactivity Prediction of SARS-CoV-2 Main Protease Inhibitors using Recurrent Neural Network-based Transfer Learning
scaffold_hopping_whales
Code to perform scaffold hopping and virtual screening using WHALES descriptors.