Protein Structure Prediction Using MODELLER: From Sequence to Validated 3D Model
Transform Protein Sequences into Reliable 3D Structures.
Skills you will gain:
About Workshop:
Protein structure is essential for understanding biological function, molecular interactions, and disease mechanisms. When experimental structures are unavailable, homology modeling provides a reliable approach by leveraging known templates from the Protein Data Bank (PDB). Accurate modeling depends on selecting suitable templates, building high-quality alignments, generating multiple candidate models, and validating structural quality before use in docking or simulation studies.
In this workshop, participants will learn a complete MODELLER workflow: sequence retrieval, BLAST-based template search, alignment building, automated model generation, loop refinement, and model ranking using scoring functions (e.g., DOPE). Participants will also validate models using standard structural checks such as Ramachandran plots and quality scores, enabling confident selection of the best 3D model for research applications.
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.
What you will learn?
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
Mentor Profile
Fee Plan
Important Dates
12 Jan 2026 Indian Standard Timing 7:00 PM
03 Feb 2026 to 05 Feb 2026 Indian Standard Timing 8:00 PM
Get an e-Certificate of Participation!
Intended For :
- 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.
Career Supporting Skills
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.