prescient-design / holo-bench
Benchmark for Biophysical Sequence Optimization Algorithms
☆13Updated 3 weeks ago
Related projects ⓘ
Alternatives and complementary repositories for holo-bench
- Code for "Biological Sequence Design with GFlowNets", 2022☆72Updated last year
- Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)☆66Updated 6 months ago
- Official repository for discrete Walk-Jump Sampling (dWJS)☆49Updated 11 months ago
- Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation☆35Updated this week
- Code for the paper Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design☆34Updated 4 months ago
- Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions☆23Updated last year
- Implementation code for the paper "Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport"☆12Updated this week
- PyTorch implementation for our paper "Proximal Exploration for Model-guided Protein Sequence Design"☆36Updated last year
- Shows some of the ways molecule generation and optimization can go wrong☆15Updated last year
- A Modular Architecture for Deep Learning Systems☆38Updated last month
- Massively-Parallel Natural Extension of Reference Frame☆30Updated last year
- Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion☆51Updated 6 months ago
- Official repository for "Plug & Play Directed Evolution for Proteins with Gradient-Based Discrete MCMC"☆11Updated last year
- This Denoising Force Field (DFF) codebase provides a Pytorch framework for the method presented in Two for one: Diffusion models and forc…☆51Updated 5 months ago
- This repository implements Gibbs sampling with Graph-based Smoothing☆36Updated 5 months ago
- Implementation of methods to sample from Boltzmann distributions☆19Updated last year
- Official repository for discrete Walk-Jump Sampling (dWJS)☆45Updated 5 months ago
- A diffusion model for structure-based drug design with faster inference from learned representations of protein structure.☆25Updated 11 months ago
- In-silico design pipeline for evaluating protein structure diffusion models.☆16Updated 4 months ago
- Repository for Fast Non-autoregressive Inverse Folding with Discrete Diffusion☆14Updated 9 months ago
- protein backbone refinement☆14Updated 2 months ago
- HyperPCM: Robust task-conditioned modeling of drug-target interactions☆36Updated last month
- Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.☆25Updated 8 months ago
- Source code for ICLR 2021 paper: "Molecule Optimization by Explainable Evolution"☆28Updated 3 years ago
- Code for the paper Iterated Denoising Energy Matching for Sampling from Boltzmann Densities.☆41Updated 9 months ago
- RetroBridge: Markov Bridge Model for Retrosynthesis Planning☆26Updated 7 months ago
- GeneDisco is a benchmark suite for evaluating active learning algorithms for experimental design in drug discovery.☆36Updated last year
- Lagrangian formulation of Doob's h-transform allowing for efficient rare event sampling☆39Updated this week
- Code for the paper https://arxiv.org/abs/2402.04997☆57Updated 9 months ago
- Source code for RNA-FrameFlow: SE(3) Flow Matching for 3D RNA Backbone Design☆31Updated last week