ur-whitelab/md-agent

Stars
67
Rank 462,689 (Top 10 %)
Language
Python
License
MIT License
Created over 1 year ago
Updated 3 months ago

ur-whitelab/md-agent

ur-whitelab

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Molecular dynamics simulations with an LLM agent

chemcrow-public

exmol

Explainer for black box models that predict molecule properties

Jupyter Notebook

LLMs-in-science

BO-LIFT

BayesOpt + LIFT

Jupyter Notebook

chemcrow-runs

Jupyter Notebook

wazy

Bayesian Optimization with Pretrained Protein Sequence Models

Jupyter Notebook

nmrgnn

Graph neural network for predicting NMR chemical shifts

hoomd-tf

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

peptide-dashboard

Web cards/apps describing peptides

Jupyter Notebook

maxent

MaxEnt code for fitting simulation outcomes/statistical models to observations

Jupyter Notebook

mol.dev

Jupyter Notebook

nmrdata

nlcc-data

Benchmark dataset and evaluation for large language models that generate code

Jupyter Notebook

alcfd

Active learning symbolic regression CFD + AI = Wow

peptidesim

Automated peptide simulation tool with gromacs, gromacswrapper, plumed

peptide-ai

Jupyter Notebook

simview

A VR/AR client for visualizing molecular dynamics with Unity, Hoomd

fedchem

mapping-graph

joint-chem-space

whitelab-slides

Our reveal.js slide template

parser-bench

py0

Jupyter Notebook

library-analysis

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

docker-images

A suite of Docker images used for computational chemistry

tutorials

Docker based tutorials for minimal biasing simulation methods

peptide-qspr

pu-peptides

Positive unlabeled screening with peptides

Jupyter Notebook

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.

arc-graphics