Code for the paper "State-of-the-Art Estimation of Protein Model Accuracy using AlphaFold" (https://www.biorxiv.org/content/10.1101/2022.03.11.484043v3). Experiments were run using the latest AlphaFold github commit as of 5/16/2022 (https://github.com/deepmind/alphafold on…
The main features of jproney/af2rank are: Structure Prediction Based Design.
Open-source alternatives to jproney/af2rank include: bene837/af2seq — Create a conda enviroment: conda env create -f environment_cpu.yml. clareaulab/denovo-cart-reproducibility — LLab repo for reproducing de novo CAR T manuscript files. gjoni/trdesign — The package summarizes developments on the use of trRosetta structure prediction network for various protein design… ibm/afdistill — We propose to apply knowledge distillation to the confidence metrics of the AlphaFold model, such as pTM or pLDDT… khondamirrustamov/foldcraft — Fold-conditioned de novo binder design FoldCraft enables fold-conditioning of binder structure, enabling design of… baaihealth/opencomplex — OpenComplex is an open-source platform for developing protein and RNA complex models. Based on DeepMind's Alphafold 2…
Create a conda enviroment: conda env create -f environment_cpu.yml
LLab repo for reproducing de novo CAR T manuscript files
The package summarizes developments on the use of trRosetta structure prediction network for various protein design applications. We provide core codes for the following papers:
OpenComplex is an open-source platform for developing protein and RNA complex models. Based on DeepMind's Alphafold 2 and AQ Laboratory's OpenFold, OpenComplex support almost all features from Alphafold 2 and OpenFold, and introduces the following new features: Reimplemented Alphafold-Multimer…