Datasets: AFsample2 predicts multiple conformations and ensembles with AlphaFold2

Directory Overview An overview of the directory structure, along with a description of each folder and its contents. Extract as follows. tar --use-compress-program=unzstd -xvf analysis_results.tar.zst tar --use-compress-program=unzstd -xvf input_datasets.tar.zst tar --use-compress-program=unzstd -xvf generated_models.tar.zst 1. analysis_results Contains results (.csv) of ensemble analysis Files required to generate images for the manuscript with included summarize.ipynb notebook (updated notebook available at https://github.com/iamysk/AFsample2/blob/main/notebooks/summarize.ipynb) tar --use-compress-program=unzstd -xvf analysis_results.tar.zst └── analysis_results ├── general ├── oc23 │ ├── afsample2 │ ├── SPEACH_AF │ ├── ... └── tp16 ├── afsample2 ├── SPEACH_AF ├── ... 2. generated_models This directory stores models generated during the project. It is organized by dataset names (e.g., oc23, tp16). Inside generated_models: oc23 and tp16: Subdirectories corresponding to models corresponding to various methods (AFcluster, AFsample, AFsample2, MSA subsampling, SPEACH_AF) employed in the study. All methods except AFcluster have been implemented in AFsample2 code. tar --use-compress-program=unzstd -xvf input_datasets.tar.zst └── input_datasets ├── oc23 │ ├── fastas │ ├── filtered_dict.pickle # pdbids and stats for states │ ├── msas # in .pkl format │ └── pdbs # All reference pdbs used in the study └── tp16 ├── fastas ├── msas └── pdbs 3. input_datasets Contains raw input datasets used for analysis and model generation. Organized by dataset names (e.g., oc23, tp16). Inside input_datasets (oc23 and tp16): fastas: Directory containing FASTA sequence files. filtered_dict.pickle (in oc23 only): A Python pickle file with preprocessed or filtered data. msas: Multiple Sequence Alignments (MSAs) in .pkl format used as input for modeling. pdbs: PDB structure files related to the datasets. tar --use-compress-program=unzstd -xvf generated_models.tar.zst └── generated_models ├── oc23 │ ├── afsample2 │ ├── SPEACH_AF │ ├── ... └── tp16 ├── afsample2 ├── SPEACH_AF ├── ... Citation If you use this dataset, please cite the associated publications.