De novo design of small beta barrel proteins
Year: 2022
Type: article
Abstract: This dataset contains the supplementary materials for "De novo design of small beta barrel proteins" Datasets. All dataset_SX.tar.gz files extract into a directory named data_archive. Dataset S1 (dataset_S1.tar.gz). Contains designs, input files (including blueprints, constraints, resfiles, and Rosetta xml scripts), commands, and selection scripts for Batch1-5 designs. data_archive/batch1 data_archive/batch2 data_archive/batch3 data_archive/batch4 data_archive/batch5 Dataset S2 (dataset_S2.tar.gz). Contains sequences, designs, input files (including blueprints, constraints, resfiles, and Rosetta xml scripts), commands, selection scripts, and TrRosetta and DeepAccNet (DAN) scores for chip library designs. data_archive/chip Dataset S3 (dataset_S3.tar.gz). Contains chip library protease stability assay data including sequence counts, protease EC50 and stability scores, selection results (experiments.csv), and experimental meta data. data_archive/protease_assay Dataset S4 (dataset_S4.tar.gz). Contains the LASSO regression model and feature data used for training from the chip library protease stability screen results and for predicting protease stability for the constrained hallucinated designs. data_archive/lasso_regression_model Dataset S5 (dataset_S5.tar.gz). Contains the mass spectrometry barcode library data (skyline.csv). data_archive/ms_barcodes Dataset S6 (dataset_S6.tar.gz). Contains common input files, the fragment database in HDF5 format used for structure profiles (PSSMs), command and inputs for Rosetta design filter metrics, and a script to extract DeepAccNet (DAN) scores. data_archive/common_inputs data_archive/databases/ss_grouped_vall_all.h5 data_archive/filter data_archive/deepaccnet Dataset S7 (dataset_S7.tar.gz). Contains native small beta barrel PDB sets and the clustering script used for selection. data_archive/natives Dataset S8 (dataset_S8.tar.gz). Contains a scaffold set of 12911 designed mini-barrels which have a high probability of folding based on AlphaFold2 metrics (pLDDT > 88 and model RMSD < 2.0). data_archive/scaffolds
Authors: Kim, David E., Jensen, Davin R., Feldman, David, Tischer, Doug, Saleem, Ayesha, Chow, Cameron M., Xinting Li, Carter, Lauren, Milles, Lukas, Nguyen, Hannah, Kang, Alex, Bera, Asim K., Peterson, Francis C., Volkman, Brian F., Ovchinnikov, Sergey, Baker, David
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6969005757