Sunhwan Jo

Computational chemist. Personal blog for code and science.

Running Progress from a Decade of Strava Data

Running
Strava
Data Analysis

Pulling 11 years of Strava activities to look at aerobic fitness and race pace progression

May 6, 2026

Packing circles in 2D surface

RDKit
Reaction Library

Generating Reaction Library Compounds

Jan 20, 2022

Generating Reaction Library Compounds

RDKit
Reaction Library

Generating Reaction Library Compounds

Dec 22, 2021

Run Molecular Dynamics Simulation on Container and AWS Batch

Cloud
MD Simulation

Run MD simulation on a dockerized container and AWS Batch as a simple scheduler

Apr 27, 2021

Run Molecular Dynamics Simulation on AWS Cluster

Cloud
MD Simulation

Setup AWS cluster using parallel-cluster package and run MD simulation on the AWS cluster

Apr 17, 2021

Random Matrix Theory in Molecular Classification

machine learning
QSAR

Review Random Matrix Theory

Mar 10, 2021

Learning Molecular Representation using Graph Neural Network - Training Molecular Graph

rdkit
machine learning
graph neural network

Taking a look at how graph neural network operate for molecular representations

Mar 7, 2021

Piperazine Ring Conformation using RDKit

rdkit

Examine ring conformation of piperazine built by RDKit ETKDG algorithm

Feb 24, 2021

Learning Molecular Representation using Graph Neural Network - Molecular Graph

rdkit
machine learning
graph neural network

Taking a look at how graph neural network operate for molecular representations

Feb 20, 2021

Ligand SASA in Protein Pocket

rdkit

An example of computing Ligand SASA (solvent-accessible surface area) in protein pocket using RDKit

Feb 4, 2021

Build 3D coordinates of congeneric series

rdkit

An example of building 3D coordinates of congeneric series using RDKit

Jan 29, 2021
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