G-protein based reshaping #268
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added 30 commits
May 30, 2023 07:10
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Prolines confuse the new connection code. Also, residues are getting strewn somehow. |
added 7 commits
June 21, 2023 19:28
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🟩🟩🟩 |
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Getting some really nice docks spot checking receptors with known agonists. OR1D2_hGNAL_bourgeonal.dock.txt |
| Configurable variables include: | ||
| `$dock_metals` If true, the dock will use PDBs that end in `.metal.pdb` instead of the default `.upright.pdb`. | ||
| `$dock_retries` The number of times to retry if no poses returned. Each retry increases the energy limit. | ||
| `$bias_by_energy` TODO: This has not been implemented yet. |
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This will be important to squeeze in.
| `POLSAT` Ligand's sum polar satisfaction, a measure of polar-polar and nonpolar-nonpolar proximity; | ||
| `PCLASH` Clashes between residues of the protein, minus clashes in the original PDB model; | ||
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| `ACVTH.TMR1` thru `ACVTH.TMR7` |
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Can this be made compatible with the .rgn syntax?
primaryodors
approved these changes
Jun 22, 2023
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This PR contains a facility for coupling two proteins, altering the shape of one to conform to the other.