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
Omega100
Manufactured by Openeye Scientific Software
Sourced in Hungary
The Omega100 is a high-performance spectrophotometer designed for precise absorption and transmission measurements. It features a wide wavelength range, advanced optics, and a user-friendly interface.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using omega100
1
Conformational Sampling and Docking Preparation
2
3D Molecule Processing Pipeline
Check if the same lab product or an alternative is used in the 5 most similar protocols
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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
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
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