Homology Modelling — Template Selection & Refinement — Hands-on

Gain end-to-end skills in comparative modelling, from template search and sequence–structure alignment through model building, loop refinement and assessment. This module focuses on producing docking- and simulation-ready homology models using reproducible structural bioinformatics workflows.

Homology Modelling — Template Selection & Refinement

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Session Index

Session 1 — Template Search & Selection Strategy Session 2 — Alignments & Core Model Building Session 3 — Loop Modelling & Sidechain Refinement Session 4 — Model Assessment, Ranking & Polishing

Session 1

Fee: Rs 12800

Template Search & Selection Strategy

Sequence analysis and domain architecture

domain boundaries disordered regions signal peptides & transmembranes

Template search strategies

BLAST / PSI-BLAST HHblits / HHsearch PDB & AlphaFold DB as template sources

Template evaluation and selection criteria

sequence identity & coverage resolution / quality scores biological relevance & ligands

Session 2

Fee: Rs 16800

Alignments & Core Model Building

Pairwise and multiple sequence alignments for modelling

MAFFT / Clustal Omega profile–profile alignment alignment editing & masking

Building initial homology models

MODELLER SWISS-MODEL / Phyre2 multi-template vs single-template

Handling insertions, deletions and gaps

loop regions vs conserved core exposed vs buried changes alignment–structure consistency checks

Session 3

Fee: Rs 20800

Loop Modelling & Sidechain Refinement

Loop modelling approaches

database-based loops ab initio loop sampling flexible regions near active sites

Sidechain packing and local minimization

rotamer libraries clash removal hydrogen-bond and salt-bridge optimization

Energy refinement of homology models

restrained minimization force fields & solvation models avoiding over-refinement artifacts

Session 4

Fee: Rs 23800

Model Assessment, Ranking & Polishing

Quality assessment of homology models

DOPE / GA341 / QMEAN MolProbity / ProSA per-residue reliability scores

Ranking and selecting final models

consensus scoring functional site inspection comparison with AlphaFold predictions

Deliverables: modelling report & ready-to-use structure

final PDB with documentation alignment and template set QC plots & decision log

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Homology Modelling Template Selection & Refinement Training | Comparative Modelling Workflows

Homology Modelling — Template Selection & Refinement — Hands-on