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Can semiempirical methods be used for high throughput screening (for enzyme mutants)?
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Can semiempirical methods be used for high throughput screening (for enzyme mutants)?
1.
Can semiempirical methods be used for high throughput screening?* (for enzyme mutants) Jan H. Jensen, University of Copenhagen Feel free to tweet, record, … #CompChemGRC *Dunno yet, trying to find out Here’s a status report @janhjensen 1
2.
An early attempt Turning a lipase into a amidase Verdict: so-so Only PM6 predicts correct mechanism Hediger PLOS ONE 2013 Hediger
PeerJ 2013 MOZYME in MOPAC 2 1 mutant per core per ~24-32 hrs
3.
An early attempt Turning a lipase into a amidase Verdict: no mutants with high amidase activity 👍 👎 Hediger PLOS ONE
2013 Hediger PeerJ 2013a 👍 👎 High throughput screening identifies potentially interesting mutants for further study 3
4.
Optimizing a xylanase for synthetic substrate Vedict: ?? Hediger PeerJ
2013b All possible single mutants Select double mutants 4
5.
Need PM6 in “open source” program to proceed Implementing PM6 in GAMESS PM6 & DFTB now in AmberTools PM6 up to Fluorine ✔ PM6/PCM up to F ✔ PM6-D3H+ ✔ PM6 for > F Linear scaling PM6 QM/MM PM6 Kromann unpublished Svendsen PLOS ONE
2013 Kromann PeerJ 2014 Linear scaling DFTB ✔ DFTB/PCM ✔ QM/MM DFTB Nishimoto CPL 2015 Nishimoto JPCA 2016 5
6.
How accurate are PM6 and DFTB for enzyme barrier heights? Verdict: 4(ish) out of 5 for both methods Kromann, Cui PeerJ 2016 Himo: B3LYP/6-311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) PM6 ✔ DFTB ✔PM6 ✔ DFTB ✘ PM6 ✘ DFTB ✔ PM6 ✔ DFTB ✔ PM6 ✔ DFTB ✔ 6
7.
Can semiempirical methods be used for high throughput screening? pKa prediction Verdict: OK(ish)
Jensen Arxiv 2015 Kromann PeerJ 2016 Amines 7
8.
Can semiempirical methods be used for high throughput screening? pKa prediction Jensen arXiv
2015 Kromann PeerJ Preprints 2016 ChemAxon Et3N Ref a Ref b Experiment 9.1 -0.2 0.1 0.7 4.2 Ref a Ref b CPU time ~3 min/core /conformer PM6/COSMO 8
9.
Can semiempirical methods be used for high throughput screening? Open questions/challenges How to routinely handle 1000s of molecules? (I need to learn cheminformatics) Efficient conformer search for proteins? Automatic & robust TS search? Improve accuracy by machine learning? machine learning + (DLNPO) CCSD(T) = new semiempirical
methods? Multipurpose or problem-specific methods? Experimental validation/competition (Must be better (& faster) than experimental high throughput) 9 Guallar Zimmerman, +… von Lilienfeld Reiher
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