Discover @PatWalters Open Source projects

PatWalters

Stars
1,385
Global Rank 22,396 (Top 0.8 %)
Followers 543
Following 11
Registered about 12 years ago
Most used languages

Jupyter Notebook
75.0 %

Python
18.3 %

R
5.0 %

HTML
1.7 %

practical_cheminformatics_tutorials

Practical Cheminformatics Tutorials

Jupyter Notebook

369

resources

A Highly Opinionated List of Open Source Cheminformatics Resources

172

rd_filters

A script to run structural alerts using the RDKit and ChEMBL

Python

111

useful_rdkit_utils

Some useful RDKit functions

Jupyter Notebook

chem_tutorial

Jupyter Notebook

workshop

Jupyter Notebook

Free-Wilson

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

Python

Thompson Sampling

Jupyter Notebook

solubility

An implementation of Delaney's ESOL method using the RDKit

Python

practical_cheminformatics_posts

Practical Cheminformatics Blog Posts

Jupyter Notebook

practicalcheminformatics

Jupyter Notebook

metk

Model Evaluation Toolkit

Python

fragment_expansion

Software tools for fragment-based drug discovery (FBDD)

Jupyter Notebook

kmeans

K-means clustering

Jupyter Notebook

sfi

An implementation of the Solubility Forecast Index (SFI)

Jupyter Notebook

Learning_Cheminformatics

Resources for Learning Cheminformatics with the RDKit

Jupyter Notebook

chembl_sim

ChEMBL Similarity Search

Python

interactive_plots

Interactive plots with chemical structures

Python

EFMC

Code to accompany "Practical Cheminformatics With Open Source Software"

Jupyter Notebook

silly_walks

Identifying silly molecules

Jupyter Notebook

yamc

Yet another ML method comparison

Jupyter Notebook

rapids_cheminformatics

Some demos using Nvidia RAPIDS for Cheminformatics

Jupyter Notebook

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"

dissecting_hype

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

Jupyter Notebook

comparing_classifiers

Some ideas on methods for comparing classification models

Jupyter Notebook

clusterama

Jupyter Notebook

cadd_grc_2013

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

drug_like

Comparing methods for identifying drug-like molecules

Jupyter Notebook

CADD_GRC_2019

Slides from my 2019 CADD GRC Talk

transformer

Transformer Search code

Jupyter Notebook

faiss_kmeans

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

Python

protein_tools

Jupyter Notebook

mpro_analysis

Code to accompany my blog post Analyzing the SARS-CoV-2 Main Protease (MPro) Structures

Jupyter Notebook

antibiotic

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

Jupyter Notebook

benchmark_gp

Benchmarking Gaussian Process Regression on the MoleculeACE dataset

Jupyter Notebook

torchdrug_examples

Jupyter Notebook

beyond_lipinski

Looking at drug properties over time

Jupyter Notebook

sali

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

Jupyter Notebook

qsar

Simple ML model for performing QSAR

Python

exploring_sars_cov2

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

Jupyter Notebook

FEP_TI_Comparison

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

Jupyter Notebook

interaction_fingerprints

Some experiments with interaction fingerprints

Jupyter Notebook

ring_systems

Tools for identifying ring_systems

Jupyter Notebook

escher

Code for assigning molecular symmetry

Jupyter Notebook

compare_regression

Tools for comparing regression models

Jupyter Notebook

neighbors

batch search for compound neighbors

Python

datafiles

benchmark_map4

Benchmarking the MAP4 fingerprint in regression models

patwalters.github.io

casp

plotting_distributions

Code to accompany my blog post on plotting distributions

notebook_share

gpu_kmeans

reaction_transform_reagets

Expanding reagent space with simple, one-step reactions

eval_wildwood

A quick evaluation of WildWood: a new Random Forest algorithm

rapids_test

some notebooks for testing RAPIDS

Jupyter Notebook

ml_drug_discovery_validation_sets

Validation sets, and associated commentary, for machine learning in drug discovery

acs_spring_2019_acid_base

Jupyter Notebook

az_colab

Collaboration with David

Jupyter Notebook

tag-link

Tag and link are utilities for command-line molecular design

Python

ngfp_benchmark

Benchmark Tests of Neural Graph Fingerprints

Jupyter Notebook

som

Self-Organizing Maps

Jupyter Notebook

molfeat_llm_examples

Some explorations of LLMs using Molfeat

Jupyter Notebook

jcamd_model_comparison

Code to accompany Comparing Classification Models - A Practical Tutorial

Jupyter Notebook

mutiple-comparisons

Code to accompany my blog post Multiple Comparisons, Non-Parametric Statistics and Post-Hoc Tests

Jupyter Notebook

dataviz-acs-fall-2015

Code to accompany my talk "Integrating data visualization into the drug discovery workflow" at ACS Boston 2015

PatWalters

Top repositories