shekfeh

proteus

A computational methods and simulation toolkit

genie2

Protein structure diffusion model for unconditional protein generation and motif scaffolding

Umol

Protein-ligand structure prediction

InChI

Main InChI repository

Fourier-Transform-Visualization

Demonstration of Fourier and Fast Fourier Transform over several different signals.

Poisson-Equation

A web app solving Poisson's equation in electrostatics using finite difference methods for discretization, followed by gauss-seidel methods for solving the equations. Dirichlet conditions and charge density can be set.

QLearning

Some Experiments with QLearning

Game-of-Life

Conway's Game of Life

Complex-Functions

An interactive for visualizing complex functions based on a 3Blue1Brown video and also estimation of Riemann Zeta Function using Euler Maclaurin Summation.

nmrML

nmrML is an open mark-up language for NMR data. This is the official repository for development of the nmrML schema and NMR ontology.

Tools

MetFrag

Repo hosting the MetFrag website

streamlit_prophet

Streamlit app to train, evaluate and optimize a Prophet forecasting model.

autograd

Efficiently computes derivatives of numpy code.

jax

Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

jax-md

Differentiable, Hardware Accelerated, Molecular Dynamics

LLMs4Science-Community.github.io

LLMs4Science: an open exchange of ideas to spur foundational research and LLM-enabled breakthroughs across scientific disciplines

useful_rdkit_utils

Some useful RDKit functions

mace

MACE - Fast and accurate machine learning interatomic potentials with higher order equivariant message passing.

protein-transformer

Implement, train, tune, and evaluate a transformer model for antibody classification with this step-by-step code.

visualizer

mol-demo

streamlit-ketcher

Chemical molecule custom component for Streamlit apps

PC_plus

Compute hydration free energy using 3D-RISM with PC+ correction

PDB_cleaner

A Python 3 script for cleaning up the PDB file

jupyterlabpymolpysnips

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

books

A collection of Mathematics + CS + what have you related books collected over the years for school 🎓 and personal reading 📚.

MolPainter

A Tool for Drawing Complex Planar Molecular Systems of Arbitrary Composition and Placement

MD_methods-and-analysis

Repository for MD methods and analysis from submitted or published work