Info

Feature, model parameters and prediciton results for  BioRixv manuscript titled "SPIRED-Fitness: an end-to-end framework for the prediction of protein structure and fitness from single sequence".

For source code and detailed instructions on usage, please refer to our GitHub.

If you want to quickly use our tool, you can utilize our web server for SPIRED-Fitness and SPIRED-Stab.

Feature

cDNA_dataset_FoldX_structure.zip

Mutant structure (PDB file) of each entry in cDNA proteolysis dataset generated by FoldX

Model

Note:  Only model parameters are available. For detailed instructions on usage, please refer to our GitHub.

model.zip 

• SPIRED-Fitness.pth
• SPIRED-Stab.pth

SPIRED Predicted Structure

CAMEO.tar.gz

Inference results for CAMEO targets (August 2022∼August 2023), consisting of 680 protein chains with the length ranging from50 to 1,126 residues.

Including predicted and label PDB files and tables for TM-score, lDDT & RMSD information.

CASP15.tar.gz

Inference results for 45 target domains from the CASP15 competition.

Including predicted and label PDB files and tables for TM-score, lDDT & RMSD information.

SCOPe.tar.gz

Inference results for 1,231 folds (34,021 domains) from SCOPe database (v2.08, S95, September 2021).

Including predicted PDB files and tables for TM-score, lDDT & RMSD information.

CATH.tar.gz

Inference results for 1,223 topologies (24,183 domains) from CATH database (v4.2, S35, July 2017).

Including predicted PDB files and tables for TM-score, lDDT & RMSD information.

Fitness Prediction Results

Fitness_single_mutation_pred.csv

SPIRED-Stab Training Dataset

training_set.zip

• ddG_training_dataset.csv
• dTm_training_dataset.csv

Stability Prediction Results

stability_pred.zip

• ddG_S669_pred.csv
• ddG_S461_pred.csv
• dTm_S557_pred.csv