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 This repository includes the following protein entries: Tf1beta_atp / Tf1beta_apo: the β subunit of F₁-ATPase from thermophilic Bacillus (TF₁β) in ATP-bound and apo conditions PGK_adp3pgmg / PGK_apo: phosphoglycerate kinase (PGK) in ADP-, 3PG-, and Mg-bound and apo conditions sTnC_N_2ca / sTnC_N_apo: the N-terminal domain of skeletal Troponin C in Ca²⁺-bound (two ions) and apo conditions dynamin1_GGfusion_gtp / dynamin1_GGfusion_apo: the dynamin 1 GTPase–GED construct in GTP-bound and apo conditions OxlT_oxl / OxlT_apo: OxlT in oxalate-bound and apo conditions NarK_no3 / NarK_apo: NarK in nitrate-bound and apo conditions MurJ_apo: MurJ in the apo condition CRBN-DDB1_apo: CRBN-DDB1 complex in the apo condition For each protein, all output files are compressed into a single tar.zst 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 subdirectories ("af2-msa-subsampling" (AF2 MSA subsampling) only for the apo condition; "af3-msa-subsampling" (AF3 MSA subsampling) ; and "af3-red" (AF3-ReD)), which include the output files produced by each method. Within each "af2-msa-subsampling" and "af3-msa-subsampling", additional subdirectories follow the naming format "msa<MSA depth>". Here, <MSA depth> represents the MSA depth used for structure prediction. 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>". Here, <sigma> and <weight> represent the width and strength of the Gaussian biasing potential, respectively. For "Tf1beta_atp" and "OxlT_oxl", the "af3-red" directory further includes subdirectories with prefixes "norestrict_" (indicating that the biasing potential was constructed using all predicted structures), "tlim<tlim>_" (cutoff time <tlim>), and "n<nsmooth>_" (number of adjacent Cα atoms used for smoothing <nsmooth>).