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A Python client for the ClassyFire API for chemical compound classification.

Python 5 Updated Jan 11, 2025
Jupyter Notebook 7 1 Updated Jun 3, 2024

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

Python 75 14 Updated Jan 9, 2025

A PyTorch library for implementing flow matching algorithms, featuring continuous and discrete flow matching implementations. It includes practical examples for both text and image modalities.

Python 1,737 69 Updated Jan 2, 2025

Treeffuser is an easy-to-use package for probabilistic prediction and probabilistic regression on tabular data with tree-based diffusion models.

Jupyter Notebook 38 4 Updated Dec 2, 2024
Python 2 Updated Aug 7, 2024

High-performance operations for neural network potentials

C++ 88 18 Updated Jul 10, 2024
Python 10 Updated Dec 18, 2024

Explicit crosslinks in AlphaFold 3

Python 13 2 Updated Dec 5, 2024

Serializing molecule 3D structures

11 Updated Nov 27, 2024

PREVENT: PRotein Engineering by Variational frEe eNergy approximaTion

Python 9 Updated Jul 4, 2024

Because we don't want a jupyter notebook mess...

Python 59 2 Updated Dec 18, 2024

A 15TB Collection of Physics Simulation Datasets

Jupyter Notebook 713 48 Updated Dec 18, 2024

Official repository of GENzyme

Python 40 5 Updated Nov 29, 2024

PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

Python 31 1 Updated Oct 9, 2024

Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2024).

Python 50 4 Updated Jan 7, 2025

Code for ProSST: A Pre-trained Protein Sequence and Structure Transformer with Disentangled Attention.

Python 71 5 Updated Jan 7, 2025

SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

Python 121 9 Updated Jan 2, 2025

Automated Adaptive Absolute alchemical Free Energy calculator

Python 77 9 Updated Jan 8, 2025

Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)

Python 21 3 Updated Jan 11, 2025

CoralRing is an ultra-low-latency, lock-free, garbage-free, batching and concurrent circular queue (ring) in off-heap shared memory for inter-process communication (IPC) in Java across different JV…

Java 183 9 Updated Jan 9, 2025

Metric Space Magnitude Computations

Jupyter Notebook 5 Updated Jan 10, 2025

P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching

Python 25 1 Updated Dec 18, 2024
Python 3 Updated Sep 30, 2024

Repository of Quantum Datasets Publicly Available

Python 40 3 Updated Nov 14, 2024

Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

Python 140 9 Updated Nov 21, 2024

Mixed continous/categorical flow-matching model for de novo molecule generation.

Python 85 5 Updated Jan 4, 2025

Code for ApoDock

Python 14 Updated Jan 9, 2025
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