Computational Enzymology & Protein Engineering Training | Catalytic Sites, ΔΔG Predictions, Variant Design

Engineer enzymes in silico: annotate catalytic sites, analyze substrate binding, design mutations for stability/activity, predict ΔΔG and hotspots (FoldX/Rosetta) , and build reproducible engineering reports.

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Computational Enzymology & Protein Engineering — Hands-on

Design better enzymes with structure-guided, computation-first workflows. Identify catalytic residues, model substrate poses, predict mutation effects on stability/activity, and plan focused variant sets with transparent, reproducible reporting.

Computational Enzymology & Protein Engineering

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Session Index

Session 1 — Catalytic Sites & Mechanistic Context Session 2 — Mutations: Stability/Activity Predictions Session 3 — Design Workflows & Variant Prioritization Session 4 — Mini Capstone: Engineer → Justify → Report

Session 1

Fee: Rs 6300

Catalytic Sites & Mechanistic Context

Identify catalytic residues, cofactors and motifs; map conservation

Catalytic Site Atlas BRENDA InterPro/PROSITE ConSurf

Substrate binding & pocket characterization

fpocket PLIP/LigPlot+ electrostatics (APBS)

Kinetic/thermodynamic intuition for engineering

kcat/Km context pKa shifts stability vs activity tradeoffs

Session 2

Fee: Rs 8400

Mutations: Stability/Activity Predictions

In silico mutagenesis & ΔΔG predictions (stability)

FoldX Rosetta ddG PoPMuSiC/DynaMut2

Catalytic residue sensitivity & activity proxies

contact/packing metrics electrostatic shifts substrate pose impact

Filter, rank, and sanity-check candidate variants

hotspot maps stability windows tradeoff plots

Session 3

Fee: Rs 11200

Design Workflows & Variant Prioritization

Rational & semi-rational design strategies; saturation hotspots

HotSpot Wizard FireProt RosettaDesign*

Substrate docking/pose checks to guide mutations

Vina/Smina PLIP contacts catalytic geometry

Prioritization panels & experiment-ready variant sets

multi-objective ranking risk flags variant tables

Session 4

Fee: Rs 14000

Mini Capstone: Engineer → Justify → Report

Propose variants for improved stability/activity and justify with evidence

Theory + Practical

Build an experiment-ready candidate table with provenance

ΔΔG panels contact/electrostatic maps config & scripts bundle

Deliverables: figures, tables, README & manifest

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