Raw data for "Enhanced sampling of protein conformations in AlphaFold3 with repulsive bias in the diffusion generative model"

This repository contains the protein structures generated using AF3 MSA subsampling and AF3-ReD, which are modified versions of AlphaFold3 distributed under the CC BY-NC-SA 4.0 license. This dataset follows the same license. The following software packages were used in this study: AF3 MSA subsampling: https://github.com/OkazakiLab/af3_mmm AF3-ReD: https://github.com/OkazakiLab/af3_red For each protein, all output files are compressed into a single tar.gz archive. Note that the prediction confidence JSON files are not included in this repository due to their large file size. After extraction, each archive consists of two subdirectories, af3-msa-subsampling and af3-red, which include the output files produced by each method. Within each af3-msa-subsampling, additional subdirectories follow the naming format msa<MSA depth>_<ligand>. Here, <MSA depth> represents the MSA depth used for structure prediction, and <ligand> is either apo (no ligand) or the included ligand name (e.g., atp for ATP-bound forms and oxl for oxalate-bound forms). Subdirectories starting with default_ indicate that the default MSA depth was used. Within each af3-red, additional subdirectories follow the naming format s<sigma>-w<weight>_<ligand>. Here, <sigma> and <weight> represent the width and strength of the Gaussian biasing potential, respectively.