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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:
The main features of gjoni/trdesign are: Structure Prediction Based Design.
Projects with overlapping indexed features 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. ibm/afdistill — We propose to apply knowledge distillation to the confidence metrics of the AlphaFold model, such as pTM or pLDDT… jproney/af2rank — Code for the paper "State-of-the-Art Estimation of Protein Model Accuracy using AlphaFold"… 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
We propose to apply knowledge distillation to the confidence metrics of the AlphaFold model, such as pTM or pLDDT scores. Our goal is to develop a fast, end-to-end differentiable distilled model, that can then be integrated as a structural consistency regularizer for training inverse protein…
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…