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Dynamic Protein Data Bank

Python 733 180 Updated Oct 15, 2024

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

Python 514 116 Updated Jan 13, 2025

A generative model for programmable protein design

Python 710 90 Updated Apr 11, 2024

A text-guided diffusion model for crystal structure generation

Python 34 3 Updated Jan 28, 2025

Official implementation of MatterGen -- a generative model for inorganic materials design across the periodic table that can be fine-tuned to steer the generation towards a wide range of property c…

Python 928 112 Updated Jan 23, 2025

Official repository for our work on micro-budget training of large-scale diffusion models.

Python 1,195 46 Updated Jan 12, 2025

A python module for manipulating cartesian and internal coordinates.

Python 76 19 Updated Jan 29, 2025

cuEquivariance is a math library that is a collective of low-level primitives and tensor ops to accelerate widely-used models, like DiffDock, MACE, Allegro and NEQUIP, based on equivariant neural n…

Python 176 8 Updated Jan 29, 2025

GFlowNet library specialized for graph & molecular data

Python 229 44 Updated Jan 7, 2025

DFTB+ general package for performing fast atomistic simulations

Fortran 342 167 Updated Jan 28, 2025

Library for Crystal Symmetry in Rust

Rust 42 2 Updated Jan 28, 2025

Timewarp is a research project using deep learning to accelerate molecular dynamics simulation.

Python 49 4 Updated Aug 21, 2024
Python 6 1 Updated Nov 24, 2024

Official repository for the Boltz-1 biomolecular interaction model

Python 1,555 195 Updated Jan 29, 2025

MatterSim: A deep learning atomistic model across elements, temperatures and pressures.

Jupyter Notebook 299 30 Updated Jan 23, 2025

Estimates the size of a PyTorch model in memory

Jupyter Notebook 356 49 Updated Jun 3, 2020

An SE(3)-invariant autoencoder for generating the periodic structure of materials [ICLR 2022]

Python 261 100 Updated Aug 14, 2024

Crystal graph convolutional neural networks for predicting material properties.

Python 690 319 Updated Sep 6, 2021

[NeurIPS 2023] The implementation for the paper "Crystal Structure Prediction by Joint Equivariant Diffusion"

Python 100 38 Updated Jul 16, 2024

Riemannian Adaptive Optimization Methods with pytorch optim

Python 887 82 Updated Apr 28, 2024

This repository is the official code source of PPFlow: Target-Aware Peptide Design with Torsional Flow Matching (ICML2024)

Python 67 14 Updated Jan 9, 2025

code for "Riemannian Flow Matching on General Geometries".

Python 196 15 Updated Mar 13, 2024

Code for “FlowMM Generating Materials with Riemannian Flow Matching” and "FlowLLM: Flow Matching for Material Generation with Large Language Models as Base Distributions"

Python 105 12 Updated Oct 29, 2024

TorchCFM: a Conditional Flow Matching library

Python 1,430 121 Updated Jan 24, 2025

Flow-matching algorithms in JAX

Python 83 3 Updated Aug 12, 2024

Course Project for MIT 6.882- Bayesian Modeling

HTML 5 Updated May 11, 2016

Example scripts using the CSD Python API

Jupyter Notebook 63 21 Updated Jan 9, 2025

A concise and easy-to-customize reimplementation of "ChemProp" (Yang et al, 2019) in PyTorch Geometric.

Jupyter Notebook 20 6 Updated Jun 23, 2022

A library for building equivariant neural networks and a zoo of implementations & examples.

Python 31 4 Updated Aug 9, 2022

Graph Neural Network Library for PyTorch

Python 21,805 3,742 Updated Jan 30, 2025
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