Table 1.
Abbreviations for tools, software, and computational resources used in this work
| Term | References | Explanation |
|---|---|---|
| OtoSCOPE | (Shearer et al. 2010) | A deafness-specific genetic sequencing panel that targets 223 genes as of version 9 |
| DVD | (Azaiez et al. 2018) | The Deafness Variation Database, a comprehensive collection of variants for the genes sequenced by the OtoSCOPE platform |
| AlphaFold2 | (Jumper et al. 2021; Tunyasuvunakool et al. 2021) | An artificial intelligence program developed by DeepMind that predicts a protein structure starting from its amino acid sequence |
| FFX | (Schnieders 2021) | Force Field X, a software package for biophysical molecular modeling |
| OtoProtein2 | (Tollefson et al. 2019) | A novel dataset of deafness-specific protein structures developed through (1) prediction by AlphaFold2 and (2) rigorous optimization with the biophysics software package, Force Field X |
| DDGun3D | (Montanucci et al. 2022, 2019) | A computational method for predicting the change in protein stability induced by missense variants |
| ∆∆GFold | A folding free energy difference, which quantifies the degree of protein misfolding caused by a variant | |
| ∆∆GBind | A binding free energy difference, which quantifies the degree of protein binding disruption caused by a variant | |
| CADD | (Rentzsch et al. 2018) | A widely used computational tool for predicting variant deleteriousness |