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Structural Bioinformatics & Molecular Mechanics Training | Energy Functions, ENMs/NMA, Electrostatics & Solvation

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Proteomics, Structural Bioinformatics, Molecular Modeling >> Structural Bioinformatics & Molecular Mechanics Training | Energy Functions, ENMs/NMA, Electrostatics & Solvation

Structural Bioinformatics & Molecular Mechanics — Hands-on

Bridge structure and physics: learn how molecular mechanics energy functions shape conformations, how to probe motions with normal modes/ENMs, and how electrostatics/solvation govern stability and function—then turn these into clear, reproducible analyses.

Structural Bioinformatics & Molecular Mechanics
Help Desk · WhatsApp
Session 1
Fee: Rs 6300
Energy Functions & Force Fields
  • Molecular mechanics terms: bonds, angles, dihedrals, vdW, Coulomb
    • Theory
  • Protein force fields & parameterization concepts
    • AMBER ff14SB/ff19SB CHARMM36m OPLS-AA/M water/ions choices
  • Energy minimization & local landscape intuition
    • steepest/CG/L-BFGS restraints & constraints
Session 2
Fee: Rs 8400
Conformational Analysis & Normal Modes
  • Conformational space: rotamers, Ramachandran, dihedral scans
    • SCWRL torsion profiles
  • Normal mode analysis & elastic network models (ENMs)
    • GNM/ANM ProDy low-frequency modes
  • PCA of structures/trajectories & motion visualization
    • MDAnalysis/MDTraj morphs & arrows
Session 3
Fee: Rs 11200
Electrostatics, Solvation & Stability
  • Continuum electrostatics & solvation models
    • PB/GB (APBS, GB models) dielectric choices ionic strength
  • pKa shifts, salt bridges & H-bond networks
    • PROPKA/PDB2PQR network centrality
  • Stability metrics & knowledge-based potentials
    • DOPE/DFIRE overview packing & cavities
Session 4
Fee: Rs 14000
Mini Capstone: Mechanistic Story
  • Link motions, energetics and electrostatics to a functional hypothesis
    • Theory + Practical
  • Assemble a concise analysis bundle with provenance
    • ProDy/ENM outputs APBS maps config & scripts
  • Deliverables: figures, tables, README & manifest
    • PDF CSV/TSV checksums


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