Giter Site home page Giter Site logo

biodiffusion's Introduction

๐Ÿ“– Table of contents

๐Ÿ’ก Notes

  • The following lists are curated by humans, as such may be incomplete
  • We do not wish to advertize one tool over any other, but simply list the tools we are aware of in a random order
  • Any suggestions for improvements and additions are welcome as issues or pull requests
  • Projects we identify as discontinued are marked with ๐Ÿ’€ and in a section at the end
  • If you wish to include this list in a publication do so by using the link "https://github.com/biolists/biodiffusion"

โšก๏ธ Brought to you by:


Structure Design

Methods that from noise sample protein structures, e.g. backbones.

  • RFDiffusion
    • Backbone diffusion
  • Chroma
    • Backbone diffusion
  • FoldingDiff
    • Torsion angle diffusion
  • FrameDiff
    • Backbone diffusion
  • Genie
    • Backbone diffusion
  • Anand/Achim
    • Backbone or rotamer diffusion
  • ProteinSGM
    • diffusion on Ca, rotamer, and other measures

Sequence Design

Methods that from noise sample sequences, e.g. residue unmasking.

  • NOS
    • Masked residue inpaining
  • EvoDiff
    • Masked residue inpaining, conditioned on MSA or single sequence
  • ProteinGenerator
    • Sequence space diffusion
  • GraDe-IF
    • Inverse protein folding: from structure to sequence
  • Anand/Achim
    • Masked residue inpaining
  • ProteinDT
    • Conditional (from pLM & text) protein sequence generation
  • Frey/Prescient
    • MCMC single step denoising sequence
  • PepPrCLIP
    • Forward noising ESM2 representations, CLIP based sequence reconstrubction for peptide sequences

Structure Reconstruction

Methods that, given an input in modality X, impute a structure output, e.g. from image domain to PDB structure.

  • CryoDRGN
    • CryoEM structure reconstruction

Sequence Reconstruction

Methods that, given an input in modality X, impute a sequence output, e.g. from frequency domain to sequence.

  • InstaNovo
    • Given proteomics readout, reconstruct peptide sequence

Binding prediction

Methods that operate on two molecules and predict an aspect of bidning, e.g. pose

  • DiffDock
    • Small molecule binding pose
  • DiffDock-PP
    • Protein-protein binding pose
  • NeuralPLexer
    • Small molecule binding
  • DynamicBind
    • Find binding pockets on protein surfaces
    • โš ๏ธ no code available @ GitHub repo

Binding generation

Methods that generate some entity (e.g. small mol) linking or binding an input entity/entities (e.g. linker generation)

  • DiffLinker
    • Linker generation
  • DiffSBDD
    • Small molecule generation given pocket
  • DiffAB
    • Design antibody given antigen structure
  • DiffBP
    • Small molecule generation given pocket

Molecule generation

Methods that generate some entity (e.g. small mol) unconditionally or conditionally to target specific molecular properties (e.g. 3D molecule generation)

  • EDM
  • Diffusion Prior Bridges
  • LDM
  • GCDM

Discontinued

  • ProtDiff_SMCDiff
    • C-alpha backbone diffusion
    • According to GitHub, superseeded by FrameDiff and RFdiffusion

biodiffusion's People

Contributors

amorehead avatar biogeek avatar sacdallago avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.