De novo design of small beta barrel proteins

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