The 3D molecule processing pipeline is now disconnected from the 2D loading process, above. We now use ChemAxon’s package and the command line tool CXCALC to calculate protonation states and tautomers at or near physiologically relevant pH69 (link) in three pH tranches. These are physiological, covering roughly pH 6.4 to 8.4, high, roughly pH 8.4 to 9.0, and low, roughly pH 5.8 to 6.4. Each protomer is rendered into 3D using Jchem’s molconvert (ChemAxon, Budapest, Hungary) and conformationally sampled using Omega100 (link) (OpenEye Scientific Software, Santa Fe NM).101 Atomic charges and desolvation penalties are calculated using AMSOL 7.1102 and our previously published protocol.103 (link) Files are formatted for docking as flexibase files,70 (link), 104 (link) mol2,105 sdf,106 and pdbqt.107
Protocol detail
Conformational Sampling and Docking Preparation
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Flexibase
Physiological
Protomer
Corresponding Organization :
Other organizations : University of California, San Francisco
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Variable analysis
independent variables
- PH tranches (physiological, high, and low)
- Protonation states and tautomers calculation using ChemAxon's package and CXCALC command line tool
- 3D molecular structures rendered using Jchem's molconvert
- Conformational sampling using Omega
- Atomic charges and desolvation penalties calculated using AMSOL 7.1
- Molecular files formatted for docking (flexibase, mol2, sdf, pdbqt)
- Physiologically relevant pH range (roughly pH 6.4 to 8.4)
- Not explicitly mentioned
- Not explicitly mentioned
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