3D-QSAR (CoMFA/CoMSIA) & Alignment Strategies — Hands-on

Master end-to-end 3D-QSAR with a practical focus on alignment, field generation (CoMFA/CoMSIA) , and robust validation. You will implement conformer workflows, choose alignment references (pharmacophore, shape, common scaffold) , optimize grid/field parameters, train PLS models, and interpret contour maps to guide medicinal chemistry decisions.

3D-QSAR (CoMFA/CoMSIA) & Alignment Strategies

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Session Index

Session 1 — Conformers & Alignment Strategies Session 2 — CoMFA/CoMSIA Field Generation Session 3 — PLS Modeling, Validation & AD Session 4 — Mini Capstone: 3D-QSAR & Contours

Session 1

Fee: Rs 14800

Conformers & Alignment Strategies

Conformer generation & selection

ETKDG, MMFF/UFF minimization ensemble pruning bioactive hypothesis

Molecular alignment paradigms

common scaffold (MCS) pharmacophore-guided shape/overlay approaches

Alignment QA & sensitivity

RMSD metrics sensitivity to misalignment reference selection

Session 2

Fee: Rs 17800

CoMFA/CoMSIA Field Generation

Grid & probe setup

grid spacing & extents steric/electrostatic fields dielectric & cutoffs

CoMSIA similarity indices

steric/electrostatic hydrophobic H-bond donor/acceptor

Preprocessing & scaling

column filtering autoscaling noise reduction

Session 3

Fee: Rs 20800

PLS Modeling, Validation & AD

PLS/PLS-DA with field variables

LV selection (Q², RMSECV) model calibration region focusing

Validation & robustness

k-fold/nested CV external test set y-randomization

Applicability Domain & contours

Williams plot confidence intervals contour interpretation

Session 4

Fee: Rs 24800

Mini Capstone: 3D-QSAR & Contours

End-to-end 3D-QSAR build

Theory + Practical

Alignment comparison & sensitivity

scaffold vs pharmacophore vs shape impact on Q²/RMSE reproducible configs

Deliverables

PLS model & metrics contour maps (steric/elec/hydroph) report + scripts/notebooks

PDF

3D-QSAR (CoMFA/CoMSIA) & Alignment Strategies | Fields, PLS & Contour Interpretation

3D-QSAR (CoMFA/CoMSIA) & Alignment Strategies — Hands-on