ArticleMethods in molecular biology (Clifton, N.J.)2022
Turning Failures into Applications: The Problem of Protein ΔΔG Prediction.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe.Scientific data · 2023Article
- Stability and expression of SARS-CoV-2 spike-protein mutations.Molecular and cellular biochemistry · 2023Article
- Structural heterogeneity and precision of implications drawn from cryo-electron microscopy structures: SARS-CoV-2 spike-protein mutations as a test case.European biophysics journal : EBJ · 2022Article
- Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions.Molecules (Basel, Switzerland) · 2022Review
- A Glance into MTHFR Deficiency at a Molecular Level.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
After nearly two decades of research in the field of computational methods based on machine learning and knowledge-based potentials for ΔG and ΔΔG prediction upon variations, we now realize that all the approaches are poorly performing when tested on specific cases and that there is large space for improvement. Why this is so? Is it wrong the underlying assumption that experimental protein thermodynamics in solution reflects the thermodynamics of a single protein? Both machine learning and knowledge-based computational methods are rigorous and we know the solid theory behind. We are now in a critical situation, which suggests that predictions of protein instability upon variation should be considered with care. In the following, we will show how to cope with the problem of understanding which protein positions may be of interest for biotechnological and biomedical purposes. By applying a consensus procedure, we indicate possible strategies for the result interpretation.
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Registered trials
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