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Computer-aided drug design and computational chemistry on Nuclear Receptors and Kinases

Targets of interest:

· Nuclear Receptors
· Kinases

Techniques utilized:

  • Molecular Mechanics-based docking calculations in various levels of model complexity and estimation of relative ligand binding affinities in series of congeneric compounds (LIE, MM-GBSA and MM-PBSA approaches).
  • Molecular Dynamics simulations for the study of time-dependent phenomena and the dynamic nature of drug-receptor interactions.
  • Free Energy Perturbation (FEP) calculations for the accurate prediction of binding affinities and the interpretation of delicate variations of data resulting from biological experiments.
  • Ab-initio quantum-mechanics (QM) computations at various levels of theory for the description and study of phenomena that are beyond the limitations of the MM approach like hydrogen bond quantification and modeling of chemical reactions.
  • Optimized Virtual Screening (VS) protocols for the evaluation of in-house and public-domain compound libraries (ZINC, ChEMBL, NCI).
  • Bioinformatics tools (sequence analysis, homology model construction and validation) that assist structure-based studies of experimentally uncharacterized drug targets.
  • Pharmacophore and similarity searching, fingerprint analysis and screening, physicochemical properties calculation and ADME/Tox, 2- and 3D-QSAR coupled with sophisticated statistical analysis techniques including Multivariate Data analysis (PCA, kernel PCA, PLS, OPLS).
  • Design and administration of fully automated chemical inventories, both in their virtual and physical forms.