Conformational Landscapes — Normal Modes & Ensembles — Hands-on

Understand how proteins move across their conformational landscapes. This module connects normal mode analysis, molecular dynamics, essential dynamics and ensemble modelling so that you can characterize motions, identify functional states, and extract mechanistic insight for docking, design and allostery studies.

Conformational Landscapes — Normal Modes & Ensembles

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Session Index

Session 1 — Conformational Landscapes & Normal Modes Session 2 — MD Trajectories, PCA & Essential Dynamics Session 3 — Ensembles, Clustering & State Models Session 4 — Functional Motions, Allostery & Reporting

Session 1

Fee: Rs 19800

Conformational Landscapes & Normal Modes

Energy landscapes and conformational basins

minima, barriers and pathways native state ensembles rugged vs smooth landscapes

Normal mode analysis (NMA) foundations

Hessian matrices and eigenmodes low frequency collective motions elastic network models (ENM)

Visualizing mode motions and displacements

arrow and morph animations overlap with experimental states link to functional domains

Session 2

Fee: Rs 23800

MD Trajectories, PCA & Essential Dynamics

Preparing and inspecting MD trajectories for analysis

alignment and fitting choices removal of overall translation / rotation coordinate selection (backbone vs atoms)

Principal component analysis (PCA) of motions

covariance matrices eigenvectors and eigenvalues projection of trajectories onto PCs

Essential dynamics and free energy projections

2D landscapes along PC1/PC2 population densities and basins linking PCs to experimental observables

Session 3

Fee: Rs 27800

Ensembles, Clustering & State Models

Generating and curating conformational ensembles

downsampling long MD runs RMSD and PC based metrics removal of poorly equilibrated frames

Clustering methods for conformations

k-means and hierarchical clustering density based methods selection of representative structures

From clusters to kinetic and state models

transition counts between states basic Markov state model (MSM) ideas estimating lifetimes and transition paths

Session 4

Fee: Rs 30800

Functional Motions, Allostery & Reporting

Relating modes and ensembles to function

open–closed transitions gating and loop motions mapping motions onto active sites

Allosteric pathways and communication routes

mode based allostery indicators network and graph views of motions coupling of distant sites

Deliverables: landscape figures, ensembles & narrative

free energy maps and projections representative structures per state mechanistic story for reports and slides

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Conformational Landscapes Normal Modes & Ensembles Training | NMA, PCA, Ensembles & State Models

Conformational Landscapes — Normal Modes & Ensembles — Hands-on