Difference between revisions of "Methods section"

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If you write a paper and you use our methods, then you may want to put in the method section of your paper text that describes what we did.  
 
If you write a paper and you use our methods, then you may want to put in the method section of your paper text that describes what we did.  
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** I am working on this today 4/7/22.  Please be patient while I finish **
  
  

Latest revision as of 21:37, 7 April 2022

If you write a paper and you use our methods, then you may want to put in the method section of your paper text that describes what we did.


    • I am working on this today 4/7/22. Please be patient while I finish **


ZINC15 / ZINC20 3D building

See methods section of Sterling and Irwin, ZINC15, JCIM. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658288/

Dockable ligand databases are downloadable from ZINC (http://zinc15.docking.org), and protonation states and tautomers (Jchem v15.11.23.0, www.chemaxon.com), 3D structures (Corina v3.6.0026, www.molecularnetworks.com), conformational ensembles (omega v2.5.1.4, www.eyesopen.com)51, atomic charges52 and desolvation energies53,54 are calculated as described55.

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 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 (OpenEye Scientific Software, Santa Fe NM).101 Atomic charges and desolvation penalties are calculated using AMSOL 7.1102 and our previously published protocol.103 Files are formatted for docking as flexibase files,70,104 mol2,105 sdf,106 and pdbqt.107


ZINC22 3D building

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 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 (OpenEye Scientific Software, Santa Fe NM).101 Atomic charges and desolvation penalties are calculated using AMSOL 7.1102 and our previously published protocol.103 Files are formatted for docking as flexibase files,70,104 mol2,105 sdf,106 and pdbqt.107