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PDBCharges is a web application providing partial atomic charges of protein structures from the Protein Data Bank. The charges are computed by the semiempirical quantum mechanical methods GFN1-xTB and reproduce the PBE0/TZVP/CM5 charges. Before computation of the charges, hydrogens are added to the structure by Hydride and MoleculeKit at pH 7.2. The positions of the added hydrogens are also optimized using the GFN-FF force field.
The main page allows uploading the chosen structure from PDB. The structure must be defined by its PDB ID:
The PDB ID of the protein can be obtained directly from PDB. Here, you can search for your protein. Examples of PDB IDs, which are accepted by PDBCharges: 1alf, 2pws, or 6wlv. PDB ID can be lowercase or uppercase.
By clicking on the Get charges button, the user is redirected to the results page for that protein.
The Main page also offers three use cases – proteins, which partial atomic charges provide interesting information for the research community.
The result page includes visualisation of the charged structure and a download data section.
This information consists of the PDB ID of the structure, its number of atoms, total charge and number of atoms for which the partial atomic charge calculation failed (see Limitations). An example of the information is the following:
PDBCharges integrates Mol* viewer to show the calculated charges. The user can select three different visualisation modes:
- Cartoon, in which the colour of individual amino acids is determined by the sum of charges on its atoms.
- Surface, in which partial atomic charges of the nearest atom colour the protein surface.
- Ball & Stick, in which the individual atoms are coloured according to their partial atomic charges.
The redder the colour, the more negative the charge, and the bluer the colour, the more positive the charge. The colouring can be relative (according to the highest absolute value of a computed charge) or absolute (the user can specify the range).
The Download charges and protonated structure button allows the user to download a ZIP file containing two files, specifically:
- mmCIF file contains coordinates of the protonated structure and partial atomic charges. Details regarding partial charges are provided at the end of the mmCIF file. This section contains information about the calculation methods, atom identification, and the partial atomic charges of the atoms within the molecule.
loop_
_sb_ncbr_partial_atomic_charges_meta.id # id of the charges
_sb_ncbr_partial_atomic_charges_meta.type # type of the charges
_sb_ncbr_partial_atomic_charges_meta.method # calculation method name
1 'QM' 'GFN1-xTB/CM5 (with cutoff)'
loop_
_sb_ncbr_partial_atomic_charges.type_id # id of the charges (pointer to _sb_ncbr_partial_atomic_charges_meta.id)
_sb_ncbr_partial_atomic_charges.atom_id # atom id (pointer to _atom_site.id)
_sb_ncbr_partial_atomic_charges.charge # partial atomic charge
1 1 -0.6462
1 2 0.0888
1 3 0.4992
...
- Json file containing possible warning messages for individual residues. These warnings alert the user that the structure or calculated partial atomic charges may be incorrect. Details regarding warnings for partial charges calculation are provided in the JSON file. This section includes details about residue identification and warnings encountered during the process.
[
{
"chain_id": "A",
"residue_id": 1,
"residue_name": "ABU",
"warning": "Atom(s) O were added by PDBFixer. Charge calculation failed for atom(s) O."
},
{
"chain_id": "A",
"residue_id": 7,
"residue_name": "ACA",
"warning": "Atom(s) O were added by PDBFixer. Mapping of formal charges from Dimorphite-DL and CCD to residue failed and therefore the residue is left neutral."
}
]
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TXT file contains charges of atoms present in the protonated structure. Individual values are separated by spaces. The charges are ordered by indices of the atoms for which they were computed.
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PQR file contains information about the coordinates and charges of the protonated structure. It is similar to PDB, with the two last columns changed to partial atomic charge and atomic radius.
ATOM 1 N MET 1 -23.494 -19.088 -2.588 -0.7600 2.0000
ATOM 2 CA MET 1 -22.509 -19.864 -3.374 -0.1289 2.0000
ATOM 3 C MET 1 -21.922 -18.915 -4.401 0.6910 1.7000
ATOM 4 CB MET 1 -23.176 -21.067 -4.061 -0.4312 2.0000
ATOM 5 O MET 1 -22.699 -18.157 -4.963 -0.6850 1.4000
The calculation of partial atomic charges has three phases:
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Structure preparation involves multiple steps. Initially, the structure is corrected using PDBFixer. Hydrogens are then added with the Hydride and MoleculeKit libraries. The formal charges of the protein are determined using the Moleculekit library, while charges for hetero-residues, obtained from the CCD dictionary, are enriched with charges from Dimorphite-DL.
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Optimization of hydrogens, in which the positions of the added hydrogens are optimized using the GFN-FF force field. A divide-and-conquer approach is used to speed up the process.
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The calculation of the partial atomic charges involves determining these charges for the structure using GFN1-xTB, the semiempirical quantum mechanical method. This approach reproduces the PBE0/TZVP/CM5 charge values. A divide-and-conquer strategy is used in the process to enhance computational efficiency.
The computing part has its own repository.
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PDBCharges cannot provide partial atomic charges for structures that cannot be saved in the PDB file because they contain more than 99999 atoms. Note that structures are often stored in the PDB database without hydrogens. However, the limit of 99999 atoms is for a structure with added hydrogens.
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PDBCharges cannot provide partial atomic charges for structures that have structure or format errors. Such structures usually cannot be processed by the libraries used (e.g. MoleculeKit) or alternatively the partial atomic charge calculation does not converge for the affected atoms. If the structure is not processable by a computational library, the user is informed and receives no results. In case the partial atomic charge calculation for some atoms has not been converged, the user is informed in the Summary information on the Results page.
| OS | Version | Chrome | Firefox | Edge | Safari |
|---|---|---|---|---|---|
| Linux | Ubuntu 24.04 | 131 | 133 | 131 | n/a |
| Windows | Windows 11 | 131 | 133 | 133 | n/a |
| MacOS | Sonoma 14.2 | 130 | n/a | n/a | 17.2 |
If you encounter an error or have an idea for an improvement, please send a report to Ondrej Schindler ([email protected]) or open a GitHub issue. Thank you!