Matches in SemOpenAlex for { <https://semopenalex.org/work/W4310645193> ?p ?o ?g. }
- W4310645193 abstract "Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein-protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks to multiplex techniques. On the other hand, genomics initiatives provide a large amount of data on disease-related variants that can benefit from analyses with structure-based methods. Therefore, the computational field should keep the same pace and provide new tools for fast and accurate high-throughput ΔΔG calculations. In this context, the Rosetta modeling suite implements effective approaches to predict folding/unfolding ΔΔGs in a protein monomer upon amino acid substitutions and calculate the changes in binding free energy in protein complexes. However, their application can be challenging to users without extensive experience with Rosetta. Furthermore, Rosetta protocols for ΔΔG prediction are designed considering one variant at a time, making the setup of high-throughput screenings cumbersome. For these reasons, we devised RosettaDDGPrediction, a customizable Python wrapper designed to run free energy calculations on a set of amino acid substitutions using Rosetta protocols with little intervention from the user. Moreover, RosettaDDGPrediction assists with checking completed runs and aggregates raw data for multiple variants, as well as generates publication-ready graphics. We showed the potential of the tool in four case studies, including variants of uncertain significance in childhood cancer, proteins with known experimental unfolding ΔΔGs values, interactions between target proteins and disordered motifs, and phosphomimetics. RosettaDDGPrediction is available, free of charge and under GNU General Public License v3.0, at https://github.com/ELELAB/RosettaDDGPrediction." @default.
- W4310645193 created "2022-12-13" @default.
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- W4310645193 date "2022-12-28" @default.
- W4310645193 modified "2023-10-16" @default.
- W4310645193 title "<scp>RosettaDDGPrediction</scp> for high‐throughput mutational scans: From stability to binding" @default.
- W4310645193 cites W1607931568 @default.
- W4310645193 cites W1963697504 @default.
- W4310645193 cites W1971827772 @default.
- W4310645193 cites W1987517037 @default.
- W4310645193 cites W2001842251 @default.
- W4310645193 cites W2023333666 @default.
- W4310645193 cites W2023490488 @default.
- W4310645193 cites W2032942231 @default.
- W4310645193 cites W2044172327 @default.
- W4310645193 cites W2051978340 @default.
- W4310645193 cites W2074394454 @default.
- W4310645193 cites W2125581050 @default.
- W4310645193 cites W2150192011 @default.
- W4310645193 cites W2153025234 @default.
- W4310645193 cites W2153457180 @default.
- W4310645193 cites W2154188431 @default.
- W4310645193 cites W2154866190 @default.
- W4310645193 cites W2168275402 @default.
- W4310645193 cites W2323927982 @default.
- W4310645193 cites W2330547698 @default.
- W4310645193 cites W2342369350 @default.
- W4310645193 cites W2512645103 @default.
- W4310645193 cites W2521967673 @default.
- W4310645193 cites W2522446227 @default.
- W4310645193 cites W2536977716 @default.
- W4310645193 cites W2538176089 @default.
- W4310645193 cites W2566708720 @default.
- W4310645193 cites W2607211030 @default.
- W4310645193 cites W2610575140 @default.
- W4310645193 cites W2780523853 @default.
- W4310645193 cites W2788217325 @default.
- W4310645193 cites W2799513065 @default.
- W4310645193 cites W2885278423 @default.
- W4310645193 cites W2894573839 @default.
- W4310645193 cites W2903826068 @default.
- W4310645193 cites W2909255640 @default.
- W4310645193 cites W2911126485 @default.
- W4310645193 cites W2912599138 @default.
- W4310645193 cites W2913078802 @default.
- W4310645193 cites W2920817727 @default.
- W4310645193 cites W2927647973 @default.
- W4310645193 cites W2938415845 @default.
- W4310645193 cites W2955907474 @default.
- W4310645193 cites W2982570657 @default.
- W4310645193 cites W2982586377 @default.
- W4310645193 cites W2986342958 @default.
- W4310645193 cites W2990435446 @default.
- W4310645193 cites W3010674213 @default.
- W4310645193 cites W3029661147 @default.
- W4310645193 cites W3033369476 @default.
- W4310645193 cites W3035182496 @default.
- W4310645193 cites W3069883202 @default.
- W4310645193 cites W3087371631 @default.
- W4310645193 cites W3092344367 @default.
- W4310645193 cites W3093556707 @default.
- W4310645193 cites W3111109342 @default.
- W4310645193 cites W3111584436 @default.
- W4310645193 cites W3145217038 @default.
- W4310645193 cites W3156338030 @default.
- W4310645193 cites W3177828909 @default.
- W4310645193 cites W3180124170 @default.
- W4310645193 cites W3195375135 @default.
- W4310645193 cites W3201523286 @default.
- W4310645193 cites W3202105508 @default.
- W4310645193 cites W3211795435 @default.
- W4310645193 cites W3212434214 @default.
- W4310645193 cites W3214131546 @default.
- W4310645193 cites W3215814807 @default.
- W4310645193 cites W3216782976 @default.
- W4310645193 cites W4205480045 @default.
- W4310645193 cites W4206007286 @default.
- W4310645193 cites W4206940890 @default.
- W4310645193 cites W4211196614 @default.
- W4310645193 cites W4213235305 @default.
- W4310645193 cites W4220887281 @default.
- W4310645193 cites W4221090435 @default.
- W4310645193 cites W4223904947 @default.
- W4310645193 cites W4226027101 @default.
- W4310645193 cites W4281614237 @default.
- W4310645193 cites W4283790822 @default.