What are the best open-source alternatives to Foldingdiff?

Question 1

Accepted Answer

12 open-source projects similar to microsoft/foldingdiff, ranked by shared features. Top picks: aim-uofa/fadiff, aqlaboratory/genie, aqlaboratory/genie2, erikhartman/fk-rfdiffusion, lamm-mit/proteinmechanicsdiffusiondesign, matsagad/mres-project, meneshail/topodiff, microsoft/frame-flow, nickwoodall/helixgen, szhan227/text2protein.

Question 2

Is aim-uofa/fadiff a good alternative to Foldingdiff?

Accepted Answer

This repository contains the source code accompanying the paper:

Question 3

Is aqlaboratory/genie a good alternative to Foldingdiff?

Accepted Answer

This repository provides the implementation code for our ICML paper. Below provides an illustration of the sampling process.

Question 4

Is aqlaboratory/genie2 a good alternative to Foldingdiff?

Accepted Answer

This repository provides the implementation code for our preprint, including training and inference code, as well as model weights. For the in-silico evaluation pipeline, which is used to assess the designability, diversity and novelty of our generated structures, we provide them in a seperate…

Question 5

Is erikhartman/fk-rfdiffusion a good alternative to Foldingdiff?

Accepted Answer

Feynman-Kac guided protein design using RFdiffusion. This package implements particle filtering to optimize design objectives during the diffusion process.

Question 6

Is lamm-mit/proteinmechanicsdiffusiondesign a good alternative to Foldingdiff?

Accepted Answer

B. Ni, D.L. Kaplan, M.J. Buehler, ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model. Sci. Adv. 10, eadl4000 (2024). DOI: 10.1126/sciadv.adl4000

Question 7

Is matsagad/mres-project a good alternative to Foldingdiff?

Accepted Answer

This repository provides an interface for solving motif scaffolding problems with an unconditional diffusion model as a prior. It defines inverse problems for a variety of tasks and solves them by sampling the posterior via sequential Monte Carlo. This permits conditional sampling without…

Question 8

Is meneshail/topodiff a good alternative to Foldingdiff?

Accepted Answer

This is the official code repository of the paper "TopoDiff: Improving Diffusion-Based Protein Backbone Generation with Global-Geometry-aware Latent Encoding".

Question 9

Is microsoft/frame-flow a good alternative to Foldingdiff?

Accepted Answer

FrameFlow is a SE(3) flow matching method for protein backbone generation and motif-scaffolding. The method is described in two papers:

Question 10

Is nickwoodall/helixgen a good alternative to Foldingdiff?

Accepted Answer

Generation of Four Helix Backbones and Sequence Design via Deep Learning Pipeline

Question 11

Is szhan227/text2protein a good alternative to Foldingdiff?

Accepted Answer

A text-to-protein backbone diffusion model. 1. Build Conda environment Run command: `` conda env create -n text2protein --file env.yaml ``

Open-source alternatives to Foldingdiff

aim-uofa/FADiff

aqlaboratory/genie

aqlaboratory/genie2

ErikHartman/FK-RFdiffusion

lamm-mit/ProteinMechanicsDiffusionDesign

matsagad/mres-project

meneshail/TopoDiff

microsoft/frame-flow

NickWoodall/HelixGen

szhan227/text2protein

tomlongcool/diffusion4Protein

zaixizhang/FoldMark