Patrick Walters

practical_cheminformatics_tutorials. Practical Cheminformatics Tutorials

resources_2025. Machine Learning in Drug Discovery Resources 2024

useful_rdkit_utils. Some useful RDKit functions

resources. A Highly Opinionated List of Open Source Cheminformatics Resources

rd_filters. A script to run structural alerts using the RDKit and ChEMBL

chem_tutorial. Jupyter Notebook

TS. Thompson Sampling

practical_cheminformatics_posts. Practical Cheminformatics Blog Posts

Free-Wilson. An implementation of the Free-Wilson SAR analysis method using the RDKit

workshop. Jupyter Notebook

solubility. An implementation of Delaney's ESOL method using the RDKit

metk. Model Evaluation Toolkit

fragment_expansion. Software tools for fragment-based drug discovery (FBDD)

practicalcheminformatics. Jupyter Notebook

sfi. An implementation of the Solubility Forecast Index (SFI)

kmeans. K-means clustering

Learning_Cheminformatics. Resources for Learning Cheminformatics with the RDKit

chembl_sim. ChEMBL Similarity Search

frankenrocs. Jupyter Notebook

silly_walks. Identifying silly molecules

EFMC. Code to accompany "Practical Cheminformatics With Open Source Software"

yamc. Yet another ML method comparison

interactive_plots. Interactive plots with chemical structures

rapids_cheminformatics. Some demos using Nvidia RAPIDS for Cheminformatics

cheminformaticsbook. These files are meant to accompany "What are our models really telling us? A practical tutorial on avoiding common mistakes when building predictive models"

PatWalters.

dissecting_hype. Code to accompany my blog post "Dissecting the Hype With Cheminformatics"

faiss_kmeans. K-Means clustering of molecules with the FASS library from Facebook AI Research

comparing_classifiers. Some ideas on methods for comparing classification models

ChEMBL-Search. A simple script to extract bioactivity data from the ChEBML database

antibiotic. Reproducing results from "A Deep Learning Approach to Antibiotic Discovery"

active_learning_tutorials. In process work on active learning tutorials

clusterama. Jupyter Notebook

TS_2025. Latest Thompson Sampling validation

protein_tools. Jupyter Notebook

CADD_GRC_2019. Slides from my 2019 CADD GRC Talk

drug_like. Comparing methods for identifying drug-like molecules

patwalters.github.io. JavaScript

cadd_grc_2013. Code from my GRC talk and the subsequent hands-on session

qsar. Simple ML model for performing QSAR

beyond_lipinski. Looking at drug properties over time

sali. Using the Structure Activity Landscape Index (SALI) to view SARS-CoV-2 Main Protease (MPro) Assay Data

transformer. Transformer Search code

FEP_TI_Comparison. Further analysis of the data in https://chemrxiv.org/articles/Validation_of_AMBER_GAFF_for_Relative_Free_Energy_Calculations/7653434

DeepLearningLifeSciences. Example code from the book "Deep Learning for the Life Sciences"

sdf_search. Jupyter Notebook

exploring_sars_cov2. Code to accompany my blog post Examining the Data From the ChEMBL SARS-Cov-2 Drug Repurposing Screens

benchmark_map4. Benchmarking the MAP4 fingerprint in regression models

RIPS. Jupyter Notebook

SMILES-RNN. Repository for SMILES-based RNNs for reinforcement learning-based de novo molecule generation

neighbors. batch search for compound neighbors

rdkit. The official sources for the RDKit library

notebook_share. Jupyter Notebook

iSIM. Module containing scripts to perform multiple comparison simultaneously and getting the exact same value as the average pairwise comparisons of molecules represented by binary fingerprints or real number descriptors.

ml_benchmark. Jupyter Notebook