White Laboratory (@ur-whitelab)
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Top repositories

1

chemcrow-public

Chemcrow
Python
583
star
2

exmol

Explainer for black box models that predict molecule properties
Jupyter Notebook
280
star
3

LLMs-in-science

138
star
4

md-agent

Molecular dynamics simulations with an LLM agent
Python
67
star
5

BO-LIFT

BayesOpt + LIFT
Jupyter Notebook
63
star
6

chemcrow-runs

Jupyter Notebook
62
star
7

wazy

Bayesian Optimization with Pretrained Protein Sequence Models
Jupyter Notebook
52
star
8

nmrgnn

Graph neural network for predicting NMR chemical shifts
Python
48
star
9

hoomd-tf

A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD
Python
30
star
10

peptide-dashboard

Web cards/apps describing peptides
Jupyter Notebook
23
star
11

maxent

MaxEnt code for fitting simulation outcomes/statistical models to observations
Jupyter Notebook
16
star
12

mol.dev

Jupyter Notebook
14
star
13

nmrdata

Python
10
star
14

nlcc-data

Benchmark dataset and evaluation for large language models that generate code
Jupyter Notebook
10
star
15

alcfd

Active learning symbolic regression CFD + AI = Wow
Python
8
star
16

peptidesim

Automated peptide simulation tool with gromacs, gromacswrapper, plumed
Python
7
star
17

peptide-ai

Jupyter Notebook
6
star
18

simview

A VR/AR client for visualizing molecular dynamics with Unity, Hoomd
C#
4
star
19

fedchem

Python
4
star
20

mapping-graph

Python
4
star
21

joint-chem-space

Python
4
star
22

whitelab-slides

Our reveal.js slide template
CSS
3
star
23

parser-bench

Python
3
star
24

py0

Jupyter Notebook
3
star
25

library-analysis

Collaboration project with Rudi Fasan's group to implement a peptide library analysis tool in python and do QSAR modeling.
Python
2
star
26

docker-images

A suite of Docker images used for computational chemistry
Dockerfile
2
star
27

tutorials

Docker based tutorials for minimal biasing simulation methods
Python
2
star
28

peptide-qspr

Python
2
star
29

pu-peptides

Positive unlabeled screening with peptides
Jupyter Notebook
1
star
30

CG-Mapper

CG-Mapper is a webpage that takes in a SMILES string and shows a graphical representation that can be used to coarse grain molecules.
JavaScript
1
star
31

arc-graphics

C#
1
star