Flexible Docking & Induced-Fit Paradigms — Hands-on

Go beyond rigid docking by explicitly modeling receptor and ligand flexibility. This module focuses on induced-fit strategies, sidechain and limited backbone motion, ensemble docking and short MD or minimization based refinement so that your interaction models better reflect realistic binding events.

Flexible Docking & Induced-Fit Paradigms

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Session Index

Session 1 — Flexibility Concepts & Receptor States Session 2 — Induced-Fit Protocols & Local Refinement Session 3 — Ensemble Docking & State Sampling Session 4 — Analysis, Validation & Reporting

Session 1

Fee: Rs 18800

Flexibility Concepts & Receptor States

Why rigid docking can fail

sidechain rearrangements backbone shifts & loop motion water and protonation effects

Receptor conformational states for docking

open vs closed forms apo vs holo structures MD derived snapshots

Flexible degrees of freedom in docking engines

ligand torsions sidechain rotamers limited backbone flexibility

Session 2

Fee: Rs 22800

Induced-Fit Protocols & Local Refinement

Induced-fit concepts and workflows

sequential docking and refinement local sidechain remodeling backrub and loop relaxation

Refining binding sites around docked ligands

minimization with positional restraints hydrogen bond network optimization rotamer exploration and pruning

Practical induced-fit workflows in pipelines

rigid pre-dock → local refinement template based sidechain rebuilding automation and job control scripts

Session 3

Fee: Rs 26800

Ensemble Docking & State Sampling

Generating receptor ensembles

MD snapshots and clustering NMR models and experimental ensembles rotamer and local sampling

Running and managing ensemble docking

multiple receptor grids batch job orchestration tracking pose provenance per state

Interpreting ensemble docking outcomes

state specific vs global ranking population and occupancy ideas selecting poses for refinement

Session 4

Fee: Rs 29800

Analysis, Validation & Reporting

Contact patterns and interaction fingerprints

H bonds, hydrophobics, salt bridges water mediated contacts flexible residue hotspot mapping

Short MD and energy based validation

local MD relaxation stability of key contacts basic MM GBSA checks

Deliverables: flexible docking report & design hints

ranked poses with receptor state info figures of induced-fit changes SAR and optimization suggestions

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Flexible Docking & Induced-Fit Paradigms Training | Receptor Flexibility, Ensembles & Refinement

Flexible Docking & Induced-Fit Paradigms — Hands-on