𝛂Charges
Partial atomic charges for AlphaFold structures
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Ondřej Schindler, Karel Berka, Alessio Cantara, Aleš Křenek,
Dominik Tichý, Tomáš Raček, Radka Svobodová
AlphaFoldDB – predicted protein structures
~ 200 M protein structures
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2
AlphaFoldDB
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https://predictioncenter.org/casp14/doc/presentations/2020_11_30_CASP14_Introduction_Moult.pdf
Structure prediction challenge 2020: AlphaFold2 wins
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AlphaFoldDB
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Structural Biology Seminar
Today (2.3.) 14:00
AlphaFold and AlphaPulldown
Petr Kulhánek
P-glycoprotein
5
5
P-glycoprotein
6
6
P-glycoprotein
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Trans-
membrane
part
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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/
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 ?, submitted 18.2.2023 8
aCharges: Partial atomic charges for AlphaFold structures
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pH
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10
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aCharges: visualization DominikTichý
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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.
Examples: Pepsin in different pH values
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pH 1 pH 2 pH 3 pH 4
pH 5 pH 6 pH 7 13
ACTIVE
INACTIVE
Alessio Cantara
activity decrease
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