FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models

A trainable PyTorch reproduction of AlphaFold 3.

A conditionally adapted protein language model for the generation of enzymes

WorldCuisines is an extensive multilingual and multicultural benchmark that spans 30 languages, covering a wide array of global cuisines.

Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. https://www.biorxiv.org/content/10.1101/2024.08.06.606920v1

List of computational protein design research labs

Describe and apply transformation on molecular structures and topologies

Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.

Evolutionary couplings from protein and RNA sequence alignments

Public RFDiffusionAA repo

Biological foundation modeling from molecular to genome scale

Full-Atom Peptide Design based on Multi-modal Flow Matching (ICML 2024)

Snakemake implementation of protein structure alignment software DaliLite v5

Pretrainable geometric graph neural network for antibody affinity maturation

This is a Phi-3 book for getting started with Phi-3. Phi-3, a family of open sourced AI models developed by Microsoft. Phi-3 models are the most capable and cost-effective small language models (SL…

Protein-ligand structure prediction

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

Official Pytorch Implementation of the paper: Wavelet Diffusion Models are fast and scalable Image Generators (CVPR'23)

PLM based active learning model for protein engineering

Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion

RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching

Protein Ligand INteraction Dataset and Evaluation Resource

Notebooks and environment set up for IQB 2024 workshop - Python for Molecular Docking

[ICML 24] Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space

CUDA Templates for Linear Algebra Subroutines

RoseTTAFold2 protein/nucleic acid complex prediction

Diffusion model based protein-ligand flexible docking method