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_2025_buelow_AF-CALVADOS
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# _2025_buelow_AF-CALVADOS This repository contains notebooks to reproduce figures in S. von Buelow, K. E. Johansson, K. Lindorff-Larsen AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level bioRxiv 2025 The notebooks for the parameterisation figures and cytosol (transcription factor) figures can be found in the respective folders. To use the notebooks, additional data need to be downloaded from the corresponding ERDA repository: [Repository](https://sid.erda.dk/sharelink/gfZNiWkxRT) Individual simulations can be retrieved from a tree-structured ERDA repository: [Repository](https://sid.erda.dk/sharelink/FxaWhNrQgp) AF-CALVADOS is integrated in the [CALVADOS](https://github.com/KULL-Centre/CALVADOS) package. Single-chain simulations with AF-CALVADOS can also be run via a Google Colab: [](https://colab.research.google.com/github/KULL-Centre/_2025_buelow_AF-CALVADOS/blob/main/AF_CALVADOS.ipynb)
