Protein Structure Prediction Using MODELLER: From Sequence to Validated 3D Model
Transform Protein Sequences into Reliable 3D Structures.
Aim
This workshop aims to train participants in protein structure prediction using comparative (homology) modeling with MODELLER. It guides learners through the complete workflow from protein sequence analysis to building, refining, and validating 3D structural models. Participants will understand how sequence similarity, template selection, and model assessment influence structural accuracy. The program emphasizes practical, dry-lab skills relevant to structural biology and drug discovery.
Workshop Objectives
- Analyze protein sequences and identify suitable templates.
- Perform accurate sequence–structure alignments.
- Build 3D protein models using MODELLER.
- Refine models and address structural gaps or loops.
- Validate and interpret model quality using standard metrics.
Workshop Structure
Day 1: Homology Modeling Workflow & Building the First Model
- Homology modeling (when to use MODELLER vs AlphaFold)
- Inputs & concepts: target sequence, templates, alignment, loops
- (PDB/BLAST) & choosing the best templates (identity, coverage, resolution)
- Alignment preparation (common alignment mistakes)
- MODELLER setup: installation, environment, file formats (PIR/ALI)
- Hands-on: Build a basic homology model (single-template or multi-template)
- Tools: MODELLER, BLAST/PDB, UniProt, PyMOL/ChimeraX
Day 2: Refinement, Validation & Reporting
- Loop modeling (short loops vs difficult regions)
- Refinement overview (energy minimization idea; restraints)
- Model validation essentials:
- Ramachandran (stereochemistry)
- Verify3D / ERRAT / ProSA (quick quality checks)
- Structural comparison to template (RMSD, superposition)
- Hands-on: Loop refinement + validate and generate a “model quality report.”
- Tools: MODELLER, PyMOL/ChimeraX, PROCHECK/RAMPAGE, ProSA, Verify3D, ERRAT
Who Should Enrol?
- Doctoral Scholars & Researchers: PhD candidates seeking to integrate computational workflows into their molecular research.
- Postdoctoral Fellows: Early-career scientists aiming to enhance their data-driven publication profile.
- University Faculty: Professors and HODs interested in modern bioinformatics pedagogy and tool mastery.
- Industry Scientists: R&D professionals from the Biotechnology and Pharmaceutical sectors transitioning to genomic-driven discovery.
- Postgraduate Students: Final-year PG students looking for specialized research-grade exposure beyond standard curricula.
Important Dates
Registration Ends
01/12/2026
IST 7:00 PM
Workshop Dates
01/12/2026 – 01/13/2026
IST 8:00 PM
Workshop Outcomes
- Build accurate 3D protein models using homology modeling.
- Evaluate model quality using structural validation tools.
- Understand strengths and limitations of comparative modeling.
- Generate structures suitable for docking, MD simulations, or functional studies.
- Apply protein modeling workflows in research or industry projects.
Fee Structure
Student Fee
₹1799 | $70
Ph.D. Scholar / Researcher Fee
₹2799 | $80
Academician / Faculty Fee
₹3799 | $95
Industry Professional Fee
₹4799 | $110
What You’ll Gain
- Live & recorded sessions
- e-Certificate upon completion
- Post-workshop query support
- Hands-on learning experience
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