3D Molecule Processing Pipeline

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
pH^{69 (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 Omega^{100 (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

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Sterling T, & Irwin J.J. (2015). ZINC 15 – Ligand Discovery for Everyone. Journal of Chemical Information and Modeling, 55(11), 2324-2337.

Publication 2015

Jchem’smolconvert Omega100

Flexibase Physiological Protomer

Corresponding Organization :

Other organizations : University of California, San Francisco

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Protocol cited in 142 other protocols

Variable analysis

independent variables

Protonation states and tautomers at or near physiologically relevant pH
PH tranches (physiological, high, and low)

dependent variables

3D molecular structures
Conformational sampling
Atomic charges and desolvation penalties

control variables

Physiologically relevant pH range (approximately 6.4 to 8.4)
Jchem's molconvert for 3D rendering
Omega for conformational sampling
AMSOL 7.1 for atomic charges and desolvation penalties
File formats for docking (flexibase, mol2, sdf, pdbqt)

positive controls

Not specified

negative controls

Not specified

Annotations

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