Threading Fold Recognition and Ab Initio Modeling — Hands-on

Learn how to build structural models when close homologous templates are not available. This module covers fold recognition concepts, threading scores, contact and secondary structure guided modeling, and ab initio strategies, with a focus on hybrid workflows that produce docking and MD ready models for difficult targets.

Threading Fold Recognition and Ab Initio Modeling

Help Desk · WhatsApp

Session Index

Session 1 — Fold Recognition Concepts & Profiles Session 2 — Threading Scores & Template Decisions Session 3 — Ab Initio & Contact Guided Modeling Session 4 — Mini Capstone: Hybrid Threading Model

Session 1

Fee: Rs 8800

Fold Recognition Concepts & Profiles

When homology modeling fails and fold recognition is needed

twilight zone of sequence identity remote homology vs de novo sequence and domain architecture checks

Profiles and hidden Markov model style representations

position specific scoring matrices profile profile alignment ideas sequence family and co evolution signal

Secondary structure and topology hints for fold recognition

secondary structure prediction membrane span and disorder regions SCOP and CATH fold classifications

Session 2

Fee: Rs 11800

Threading Scores & Template Decisions

How threading methods align sequence onto structure

profile structure comparison gap penalties and alignment paths scoring matrices and contact terms

Reading and interpreting threading scores

Z scores and confidence ranks coverage and alignment quality filtering false positive folds

Choosing templates and alignment regions for modeling

core fold vs flexible regions conserved motifs and catalytic residues multi template and hybrid decisions

Session 3

Fee: Rs 14800

Ab Initio & Contact Guided Modeling

Core ideas of ab initio and fragment based modeling

fragment libraries and assembly energy landscapes and funnels ensemble of decoy structures

Contacts and distance restraints in free modeling

co evolution based contact prediction distance and orientation restraints secondary structure and topology bias

Hybrid threading plus ab initio modeling strategies

template based core plus free loops refining weakly aligned segments building missing domains or tails

Session 4

Fee: Rs 18800

Mini Capstone: Hybrid Threading Model

Select a difficult target and identify candidate folds

Theory + Practical

Build and refine a hybrid threading plus ab initio model

template based core construction ab initio loops and termini energy and clash based filtering

Deliverables: model set, confidence assessment and report

ranked PDB models per residue confidence annotation written summary of limitations and uses

PDF

Threading Fold Recognition and Ab Initio Modeling Training | Remote Homology & Hybrid Modeling

Threading Fold Recognition and Ab Initio Modeling — Hands-on