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HPC in molecular modelling

HPC in molecular modelling. Alons Lends RTU MKF Latvian Institute of Organic Synthesis. Molecular modelling. Molecular modeling  encompasses all theoretical methods and computational techniques used to  model  or mimic the behavior of molecules. Fields of use Computional chemistry

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HPC in molecular modelling

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  1. HPC in molecular modelling Alons Lends RTU MKF Latvian Institute of Organic Synthesis

  2. Molecular modelling Molecular modeling encompasses all theoretical methods and computational techniques used to model or mimic the behavior of molecules. Fields of use Computional chemistry Drug design Computional biology Material science

  3. Molecular modelling Quantum mechanics Molecular mechanics For large systems For small systems Ab initio, DFT (B3LYP,...) Different basis sets (6-31G*...) V.G. Box.J. Mol. Model.3 124–41.

  4. Carbonic anhydrase (CA) Zinc containing proteins α, β, γ, δ, ε α-CA 16 differetn isoforms KiμM - nM Linskog et al.Biochem., 1987, 26, 5293–5301 Innocenti et al. Bioorg. Med. Chem., 2010, 18,3938-3941. Supuran et al. Med. Res. Rev., 2003, 23, 146-189.

  5. Geometry comparison in active center B3LYP 631-G* X-ray structure Supuran et al. ChemMedChem., 2010, 5,1-8. Sousa et al. J. Comput. Chem., 2009, 30, 2752–2763,

  6. Quantum chemical calculations DFT B3LYP/6-31G* ΔE=E2-E1 Ligand hardness 6

  7. Other proteins containing zinc in active center Alcohol dehydrogenase Alkaline phosphatase Histone deacetylase β carbonic anhydrase Can2 α Carbonic anhydrase Matrix metalloprotease

  8. ΔE (kcal/mol) binding energy calculations

  9. NMR spectroscopy

  10. Ea=15.9 ± 0.6 kcal/mol

  11. Thank you for attention! Lauris Cikovskis and Jānis Kūliņš

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