SallyS.'s repositories
aizynthfinder
A tool for retrosynthetic planning
AMBER-Membrane_protein_tutorial
Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen
CAMP
predicting peptide-protein interactions
exmol
Explainer for black box models that predict molecule properties
GraphBP
Official implementation of "Generating 3D Molecules for Target Protein Binding"
kissim
Subpocket-based fingerprint for kinase pocket comparison
Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
molcloud
Make a bunch of molecules
molecule-generation
Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation
moleculekit
MoleculeKit: Your favorite molecule manipulation kit
nglview
Jupyter widget to interactively view molecular structures and trajectories
opencadd
A Python library for structural cheminformatics
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
plumed2
Development version of plumed 2
Pocket2Mol
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
PPIRef
Working with protein-protein interactions in 3D
ProDy
A Python Package for Protein Dynamics Analysis
ProLIF
Interaction Fingerprints for protein-ligand complexes and more
Protac-Design
UROP Project @ Coley Group
Protac-invent
A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data
protwis
Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
py-rcsb_db
RCSB Python Database Utility Classes
Pymol-script-repo
Collected scripts for Pymol
reeds
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
REMD_analysis
A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
UGM2023
Materials for the 2023 MDAnalysis User Group Meeting