Alternatives and similar repositories for holo-bench

Users that are interested in holo-bench are comparing it to the libraries listed below

• instadeepai / AbBFN2
  AbBFN2: A flexible antibody foundation model based on Bayesian Flow Networks
  ☆35Updated 5 months ago
• MJ10 / BioSeq-GFN-AL
  Code for "Biological Sequence Design with GFlowNets", 2022
  ☆74Updated 2 years ago
• kirjner / GGS
  This repository implements Gibbs sampling with Graph-based Smoothing
  ☆39Updated last year
• HeliXonProtein / proximal-exploration
  PyTorch implementation for our paper "Proximal Exploration for Model-guided Protein Sequence Design"
  ☆37Updated 2 years ago
• aqlaboratory / insilico_design_pipeline
  In-silico design pipeline for evaluating protein structure diffusion models.
  ☆27Updated last year
• Kuhlman-Lab / PIPPack
  Implementation of Protein Invariant Point Packer (PIPPack)
  ☆35Updated last year
• samuelstanton / lambo
  Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)
  ☆71Updated last year
• instadeepai / protein-sequence-bfn
  Supporting code for our paper "Protein Sequence Modelling with Bayesian Flow Networks"
  ☆47Updated 8 months ago
• Genentech / walk-jump
  Official repository for discrete Walk-Jump Sampling (dWJS)
  ☆54Updated last year
• Profluent-Internships / MMDiff
  Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
  ☆58Updated last year
• prescient-design / cortex
  A Modular Architecture for Deep Learning Systems
  ☆46Updated 5 months ago
• compsciencelab / mdCATH
  This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user ex…
  ☆49Updated 11 months ago
• EleutherAI / mp_nerf
  Massively-Parallel Natural Extension of Reference Frame
  ☆32Updated 2 years ago
• Profluent-Internships / ProCALM
  A conditionally adapted protein language model for the generation of enzymes
  ☆23Updated 11 months ago
• leojklarner / context-guided-diffusion
  Code for the paper Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design
  ☆39Updated last year
• NVlabs / protcomposer
  ☆49Updated 3 months ago
• pemami4911 / ppde
  Official repository for "Plug & Play Directed Evolution for Proteins with Gradient-Based Discrete MCMC"
  ☆12Updated 2 years ago
• flagshippioneering / flash_ipa
  [NeurIPS 2025 spotlight] Efficient factorized variant of the IPA module.
  ☆34Updated last month
• biolists / biodiffusion
  A list of manuscripts/tools using diffusion on biological enttieis
  ☆97Updated 2 years ago
• prescient-design / walk-jump
  Official repository for discrete Walk-Jump Sampling (dWJS)
  ☆58Updated last year
• hnisonoff / discrete_guidance
  Code for our paper "Unlocking Guidance for Discrete State-Space Diffusion and Flow Models"
  ☆29Updated 6 months ago
• johnyang101 / pmpnndiff
  Repository for Fast Non-autoregressive Inverse Folding with Discrete Diffusion
  ☆18Updated last year
• whitead / minimalaf
  Minimal AlphaFold
  ☆55Updated last year
• petergroth / FLOP
  This is the official code repository for the paper FLOP: Tasks for Fitness Landscapes Of Protein wildtypes by Groth et al.
  ☆22Updated 2 years ago
• LDeng0205 / confidence-bootstrapping
  Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.
  ☆27Updated last year
• rdilip / kanzi
  ☆21Updated 3 weeks ago
• rish-16 / rna-backbone-design
  Source code for RNA-FrameFlow: SE(3) Flow Matching for 3D RNA Backbone Design
  ☆80Updated 3 weeks ago
• Graylab / DFMDock
  DFMDock (Denoising Force Matching Dock), a diffusion model that unifies sampling and ranking within a single framework.
  ☆49Updated 3 months ago
• zzhangzzhang / pLMs-interpretability
  ☆30Updated last year
• adaptyvbio / ProtFill
  Inpainting protein sequence and structure
  ☆12Updated last year