Loop Modeling, Side Chain Packing & Rotamers — Hands-on

Focus on the most error prone parts of protein models: loops and side chains. This module covers loop conformations, closure and sampling strategies, rotamer libraries, packing and clash removal, and integrated refinement workflows so that active sites, interfaces and flexible regions are modeled with realistic geometry and clear quality metrics.

Loop Modeling, Side Chain Packing & Rotamers

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Session Index

Session 1 — Loops, Rotamers & Local Geometry Session 2 — Loop Modeling Strategies & Sampling Session 3 — Side Chain Packing, Rotamers & Scoring Session 4 — Active Site Refinement & Case Study

Session 1

Fee: Rs 8800

Loops, Rotamers & Local Geometry

Loop regions and local flexibility in proteins

types of loops and turns functional roles in binding and catalysis why loops are hard to model

Side chain conformations and rotamer libraries

chi angles and torsion space backbone dependent rotamers preferred states vs outliers

Local geometry, clashes and hydrogen bonds

bonded geometry basics steric clashes and overlap side chain hydrogen bond patterns

Session 2

Fee: Rs 11800

Loop Modeling Strategies & Sampling

Loop closure and kinematic approaches overview

defining anchors and loop segments closure algorithms concepts short vs long loop strategies

Template based and fragment based loop modeling

loop libraries and grafting fragment insertion around loops alignment and clash checks

Sampling, ensemble generation and constraints

energy guided loop sampling distance and dihedral constraints storing and ranking loop conformations

Session 3

Fee: Rs 14800

Side Chain Packing, Rotamers & Scoring

Rotamer optimization and packing algorithms

search over rotamer sets interaction graphs idea packing side chains in crowded regions

Detecting and fixing clashes, holes and bad contacts

clash lists and contact maps cavities and packing defects hydrogen bond and salt bridge checks

Scoring loops and side chains for reliability

rotamer outlier statistics per residue energy contributions interfaces and active site scores

Session 4

Fee: Rs 18800

Active Site Refinement & Case Study

End to end loop and side chain refinement case study

Theory + Practical

Refining active sites and binding interfaces

orienting key side chains maintaining catalytic and metal geometry preparing structures for docking or MD

Validation, reporting and figure ready panels

before and after comparisons quality summary for loops and side chains methods and limitations in manuscripts

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Loop Modeling, Side Chain Packing & Rotamers Training | Loops, Rotamers, Active Site Refinement

Loop Modeling, Side Chain Packing & Rotamers — Hands-on