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Improved Prediction of Stabilizing Mutations in Proteins by Incorporation of Mutational Effects on Ligand Binding.

Proteins - 1 Jan 2025

Ganesan Srivarshini, Mittal Nidhi, Bhat Akash, Adiga Rachana S, Ganesan Ananthakrishnan, Nagarajan Deepesh, Varadarajan Raghavan

Abstract excerpt

While many computational methods accurately predict destabilizing mutations, identifying stabilizing mutations has remained a challenge, because of their relative rarity. We tested ΔΔG 0 predictions from computational predictors such as Rosetta, ThermoMPNN, RaSP, and DeepDDG, using 82 mutants of the bacterial toxin CcdB as a test case. On this dataset, the best computational predictor is ThermoMPNN, which...

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PMID: 39166462
DOI: 10.1002/prot.26738

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