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𝛂Charges
Partial atomic charges for AlphaFold structures
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AlphaFoldDB – predicted protein structures
~ 200 M protein structures
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2

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Why partial atomic charges?
They show the chemical properties of the predicted structures
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3
P-glycoprotein

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Why partial atomic charges?
They show the chemical properties of the predicted structures
P-glycoprotein

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Trans-membrane part
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Why partial atomic charges?
They show the chemical properties of the predicted structures
P-glycoprotein

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aCharges: Partial atomic charges for AlphaFold structures
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§Computes charges for AlphaFold2 structures from AlphaFoldDB
§Method: SQE+qp, parameterized for (B3LYP/6-31G*/NPA)
§Inputs: UniProt ID of AlphaFoldDB molecules
§Outputs: plain text, mmCIF, PQR
§Visualization: Mol*
§Web page: https://alphacharges.ncbr.muni.cz/
P-glycoprotein
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Schindler O., Berka K., Cantara A., Křenek A., Tichý D., Raček T., Svobodová R, 2023. αCharges:
Partial atomic charges for AlphaFold structures in high quality. Nucleic acids research, 51(W1),
W11-W16.
issue cover

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aCharges: Partial atomic charges for AlphaFold structures
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pH
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aCharges: visualization
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Mol*
Sehnal D., Bittrich S., Deshpande M., Svobodová R., Berka K., Bazgier V., ... & Rose A. S. (2021).
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular
structures. Nucleic Acids Research, 49(W1), W431-W437.

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Examples: Pepsin in different pH values
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pH 1
pH 2
pH 3
pH 4
pH 5
pH 6
pH 7
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ACTIVE
INACTIVE
activity decrease

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Examples: PIN proteins
PIN3
PIN7
PIN5
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PIN3
PIN7
PIN5
Legend:
Similar charges
Different charges
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Examples: PIN proteins