02/01/2026

Registration closes 02/01/2026

Protein Structure Prediction Using MODELLER: From Sequence to Validated 3D Model

Transform Protein Sequences into Reliable 3D Structures.

  • Mode: Virtual / Online
  • Type: Mentor Based
  • Level:
  • Duration: 3 Days
  • Starts: 1 February 2026
  • Time: 08:00 PM IST

About This Course

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.

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

02/01/2026
IST 07:00 PM

Workshop Dates

02/01/2026 – 02/03/2026
IST 08:00 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.

Meet Your Mentor(s)

Mentor Photo

Prof. Kumud Malhotra

Professor & Dean

Prof. Kumud Malhotra, Dean of the University Institute of Physical and Life Sciences with 30 years of experience is an academician and administrator and has attained the highest echelons in the educational sector by managing senior positions, like Director, Dean, Managing Editor, or Editor-in-Chief . . . for content development and journal publication. She completed her Ph. D on “Genetic Epidemiology of Malaria in Some Population Groups of Delhi and Tribal Groups of Tarai Region of Nainital District” and Post Doctorate from Delhi University as an ICMR and UGC fellow.
Her expertise domains are Biotechnology, Genetics, Bioinformatics, Forensic  Science, Molecular Biology, and its allied areas. She has obtained Certifications in the areas of Genetic Engineering, Molecular Biology, Microarrays, Proteomics, and Parasitology from IGIB, NICD, MRC, and Delhi University. Down the lane, her achievements and accolades are the best employee and faculty while working at Bioinformatics Institute of India and RNB GLOBAL University as a Dean and other prestigious awards. Her contribution to the establishment of the School of Basic and Applied Sciences and Agricultural Sciences along with the approval from ICAR at the new University RNBGLOBAL
University was acknowledged by the Management.
Apart from teaching and academics her experience in content development and e-learning for various renowned universities and organizations like Banasthali Vidyapith, GOLS Academy, Biionline, etc. is an added credential of hers. Dr. Kumud Malhotra has been a Resource Person in Course Development Committees (for graduate and post-graduate programs) for Indira Gandhi National Open University (IGNOU), Jamia Hamdard along with other credits like Member of various committees like Academic Council, BOS, Research Committee, etc. for the IGNOU, IAMR. She has demonstrated caliber as a resourceful Technical Collaborator for the conduction of the Workshop on Bioinformatics at
Bundelkhand University and in Engineering College in Durg, Chhattisgarh with an appreciation letter from the university.
She is a member of the editorial board of various journals and has presented Papers at International Conferences on Genetics, Parasitology, Clinical Trials, Pharmacovigilance, Biotechnology, etc. Dr. Malhotra has delivered keynote addresses at CII, International Conferences, and member of various professional bodies Genetics Society, Indian Science Congress, International Society for Malariology and Parasitology, IAA, SBTI, etc. She has guided many students for Ph.D. and internships and got the projects from ICMR.

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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(+91) 120-4781-217

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