Peptide & Macrocycle Informatics — Hands-on

Master peptide & macrocycle informatics from sequence design to structure-aware screening. This hands-on module covers cyclization strategies (head-to-tail, side-chain, stapling) , conformation sampling and property prediction (permeability, polarity, proteolysis) , macrocycle descriptors, and docking/MD-lite evaluation. You will ship a reproducible pipeline to enumerate, filter, and prioritize peptide/macrocycle candidates with synthesis-aware constraints.

Peptide & Macrocycle Informatics: Design & Screening

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Session Index

Session 1 — Building Blocks, Cyclization & Enumeration Session 2 — Conformations, Descriptors & Permeability Session 3 — Docking/Scoring & MD-lite Stability Session 4 — Mini Capstone: Library → Shortlist

Session 1

Fee: Rs 20800

Building Blocks, Cyclization & Enumeration

AAs & non-canonical units

L/D amino acids N-methyl, β/γ-AAs linkers & spacers

Cyclization strategies

head-to-tail / side-chain disulfide / lactam bridges hydrocarbon stapling

Enumeration & constraints

SMARTS rules position-specific libraries synthesis-aware filters

Session 2

Fee: Rs 23800

Conformations, Descriptors & Permeability

Conformational sampling

distance geometry / ETKDG low-mode / torsion scans solvent-aware pruning

Macrocycle descriptors

PMI / 3D shape tPSA / HBD/HBA (exposed) intra-H bonds / chameleonicity

Permeability & stability

Caco-2 heuristics protease site flags serum stability hints

Session 3

Fee: Rs 26800

Docking/Scoring & MD-lite Stability

Pose generation for macrocycles

conformer → docking induced-fit (lite) constraint docking (hotspots)

Scoring & rescoring

consensus scores interaction fingerprints strain/entropy notes

MD-lite stability checks

short relax simulations H-bond & RMSD traces binding mode persistence

Session 4

Fee: Rs 30800

Mini Capstone: Library → Shortlist

Build an enumerate → sample → score → shortlist pipeline

Theory + Practical

Developability & synthesis awareness

permeability & protease risk bands stapling/disulfide feasibility vendor BB coverage

Deliverables

ranked shortlist (CSV) poses & MD-lite plots configs/notebooks for reruns

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Peptide & Macrocycle Informatics: Design & Screening | Conformations, Permeability & Stability

Peptide & Macrocycle Informatics — Hands-on