This repository contains the codebase for the paper "Leveraging ancestral sequence reconstruction for protein representation learning".
☆12Apr 13, 2025Updated 10 months ago
Alternatives and similar repositories for local-ancestral-sequence-embeddings
Users that are interested in local-ancestral-sequence-embeddings are comparing it to the libraries listed below
Sorting:
- Wrapper tool for ancestral sequence and indel reconstruction using IQ-TREE☆11Oct 20, 2025Updated 4 months ago
- Design data and process for the AdaptyvBio protein design competition☆10Dec 11, 2024Updated last year
- Protein representation and design under a single training scheme☆24Updated this week
- ☆13Sep 29, 2023Updated 2 years ago
- Ancestral Sequence Reconstruction in Python☆14May 9, 2019Updated 6 years ago
- Protein stability prediction using rewired protein generative models☆65Dec 25, 2025Updated 2 months ago
- ☆15Jun 7, 2022Updated 3 years ago
- GRACE: Generative Renaissance in Artificial Computational Enzyme Design☆19Jan 8, 2025Updated last year
- 📈 Fusion of sequence, structure and feature information to improve protein solubility prediction (IEEE BIBM 2024).☆26May 16, 2025Updated 9 months ago
- A tool for predicting the effects of missense mutations on protein stability changes upon missense mutation using protein sequence only. …☆22Jun 3, 2023Updated 2 years ago
- ☆65Apr 8, 2025Updated 10 months ago
- Utility for building inverse rotamer assemblies out of a Rosetta matcher/enzdes constraint file.☆26Mar 8, 2025Updated 11 months ago
- Biological prediction models made simple.☆49Jan 13, 2026Updated last month
- A machine-learning package for navigating combinatorial protein fitness landscapes.☆133Nov 17, 2021Updated 4 years ago
- Making Protein Language Modeling Accessible to All Biologists☆154Updated this week
- ☆33Aug 12, 2024Updated last year
- Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term☆29Dec 2, 2024Updated last year
- ☆76Aug 23, 2023Updated 2 years ago
- This is the official code repository for the paper NeurIPS 2024 spotlight paper "Kermut: Composite kernel regression for protein variant …☆42Aug 5, 2025Updated 6 months ago
- Python Implementation of Codon Adaption Index☆37Feb 1, 2023Updated 3 years ago
- This software package simulates the reduction of graphene oxide and calculates the optical response of the generated sp2 domains☆11Dec 22, 2016Updated 9 years ago
- ☆23Dec 5, 2025Updated 2 months ago
- Adaptive string method implementation in AmberTools23 and Amber22☆14Jan 7, 2025Updated last year
- ☆18Dec 5, 2024Updated last year
- Homomer symmetry prediction from protein sequence☆41Mar 13, 2025Updated 11 months ago
- ☆39Jun 12, 2025Updated 8 months ago
- Implementation of Protein Invariant Point Packer (PIPPack)☆35May 28, 2024Updated last year
- Collection of useful bioinformatic functions and tools for various computational biology pipelines☆40Updated this week
- ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models☆39Nov 25, 2024Updated last year
- Protein Design by Machine Learning guided Directed Evolution☆48Jan 1, 2026Updated 2 months ago
- Code for improving the performance of sequence-to-expression models for making individual-specific gene expression predictions by fine-tu…☆15Dec 12, 2025Updated 2 months ago
- This is for the AI enzyme design course☆13Nov 10, 2025Updated 3 months ago
- ☆14Dec 18, 2024Updated last year
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated last year
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆10Oct 2, 2025Updated 5 months ago
- DockCADD An automated computational framework for molecular docking☆15Mar 9, 2025Updated 11 months ago
- The official GitHub repository for the Nature Communications paper "Computational Design of Generalist Cyclopropanases with Stereodiverge…☆13Jan 23, 2026Updated last month
- Python Toolbox For Rosetta Silent Files Processing☆10Aug 2, 2021Updated 4 years ago
- Directed evolution of proteins in sequence space with gradients☆95Oct 18, 2025Updated 4 months ago