Ab Initio & Fold Recognition Approaches — Hands-on

Develop practical skills in structure prediction beyond classic homology modelling. This module covers fold recognition (threading) , ab initio and fragment-based modelling, plus modern contact/distance driven approaches. You will learn how to decide which strategy to use, generate models, and critically evaluate their reliability for downstream applications.

Ab Initio & Fold Recognition Approaches

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Session Index

Session 1 — Fold Recognition & Threading Basics Session 2 — Ab Initio & Fragment-Based Modelling Session 3 — Contacts, Distances & Meta-Predictors Session 4 — Model Assessment & Hybrid Strategies

Session 1

Fee: Rs 13800

Fold Recognition & Threading Basics

When homology fails: twilight zone of sequence identity

remote homologs fold vs family sequence–structure divergence

Fold recognition & threading concepts

profile–profile matching energy / scoring functions alignment–structure consistency

Practical tools and workflows

HHpred / RaptorX Phyre2 / I-TASSER fold-library selection & filtering

Session 2

Fee: Rs 17800

Ab Initio & Fragment-Based Modelling

Principles of ab initio folding

conformational search energy landscapes coarse-grained representations

Fragment libraries & assembly protocols

3-mer / 9-mer fragments secondary structure prediction driven Rosetta-style sampling

Running ab initio jobs and managing ensembles

job setup & parameters cluster / cloud execution collecting low-energy candidates

Session 3

Fee: Rs 21800

Contacts, Distances & Meta-Predictors

Co-evolution, contacts and distance prediction

MSA depth & quality contact maps distance restraints

Modern structure predictors as meta-tools

AlphaFold-style confidence metrics pLDDT / PAE maps ensembling classical & AI models

Integrating restraints into ab initio pipelines

distance- and angle-based restraints constrained sampling improving fold-level correctness

Session 4

Fee: Rs 24800

Model Assessment & Hybrid Strategies

Quality assessment for challenging models

energy vs knowledge-based scores cluster analysis of ensembles agreement with contacts/distances

Hybrid modelling strategies

threading + fragment assembly using partial templates combining experimental restraints (XL-MS, NMR)

Deliverables: prediction report & recommended model set

ranked model ensemble QC plots & contact maps narrative on model limitations

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Ab Initio & Fold Recognition Approaches Training | Threading, Fragment-Based & Contact-Driven Modelling

Ab Initio & Fold Recognition Approaches — Hands-on