Alternatives and similar repositories for holo-bench

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

• MJ10 / BioSeq-GFN-AL
  Code for "Biological Sequence Design with GFlowNets", 2022
  ☆73Updated 2 years ago
• kirjner / GGS
  This repository implements Gibbs sampling with Graph-based Smoothing
  ☆38Updated last year
• instadeepai / AbBFN2
  AbBFN2: A flexible antibody foundation model based on Bayesian Flow Networks
  ☆24Updated 3 weeks ago
• HeliXonProtein / proximal-exploration
  PyTorch implementation for our paper "Proximal Exploration for Model-guided Protein Sequence Design"
  ☆36Updated last year
• compsciencelab / mdCATH
  This repository houses all the scripts and notebooks utilized for generating, analyzing, and validating the mdCATH dataset. Some user ex…
  ☆43Updated 7 months ago
• leojklarner / context-guided-diffusion
  Code for the paper Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design
  ☆39Updated 11 months ago
• aqlaboratory / insilico_design_pipeline
  In-silico design pipeline for evaluating protein structure diffusion models.
  ☆26Updated 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
  ☆41Updated last month
• flagshippioneering / flash_ipa
  Efficient implementation of the IPA module.
  ☆28Updated 3 weeks ago
• instadeepai / protein-sequence-bfn
  Supporting code for our paper "Protein Sequence Modelling with Bayesian Flow Networks"
  ☆44Updated 3 months ago
• prescient-design / walk-jump
  Official repository for discrete Walk-Jump Sampling (dWJS)
  ☆55Updated last year
• Kuhlman-Lab / PIPPack
  Implementation of Protein Invariant Point Packer (PIPPack)
  ☆32Updated last year
• ngruver / NOS
  Protein Design with Guided Discrete Diffusion
  ☆131Updated last year
• NVlabs / protcomposer
  ☆41Updated 3 months ago
• latkins / trifast
  ☆27Updated last month
• anton-bushuiev / PPIformer
  Learning to design protein-protein interactions with enhanced generalization (ICLR 2024)
  ☆44Updated 5 months ago
• zzhangzzhang / pLMs-interpretability
  ☆27Updated 8 months ago
• Genentech / walk-jump
  Official repository for discrete Walk-Jump Sampling (dWJS)
  ☆53Updated last year
• samuelstanton / lambo
  Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)
  ☆70Updated last year
• johnyang101 / pmpnndiff
  Repository for Fast Non-autoregressive Inverse Folding with Discrete Diffusion
  ☆17Updated last year
• LDeng0205 / confidence-bootstrapping
  Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.
  ☆26Updated last year
• EleutherAI / mp_nerf
  Massively-Parallel Natural Extension of Reference Frame
  ☆31Updated 2 years ago
• instadeepai / protein-structure-tokenizer
  Official implementation of "Learning the language of protein structures"
  ☆33Updated this week
• zanderharteveld / genesis
  protein backbone refinement
  ☆15Updated 9 months ago
• 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
• leojklarner / Q-SAVI
  Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions
  ☆24Updated last year
• Dunni3 / keypoint-diffusion
  A diffusion model for structure-based drug design with faster inference from learned representations of protein structure.
  ☆29Updated last year
• VincentStimper / boltzmann-generators
  Implementation of methods to sample from Boltzmann distributions
  ☆19Updated 2 years ago
• ml-jku / mgenerators-failure-modes
  Shows some of the ways molecule generation and optimization can go wrong
  ☆17Updated last year