Lecture 06, Concept 21: Calculating Binding Free Energy - Alchemical Transformation

Lecture 06, concept 21: Calculating binding free energy - alchemical transformation

Lecture 06, concept 22: Binding free energy - the free energy cycle & DDG values

Alchemical Transformations (introduction) | Free energy estimates | Molecular Dynamics MD

The Computational Chemist

Lecture 13, concept 01: Free energy calculation provides good relative binding free energies

Lecture 06, concept 01: From static structures to simulations

Lecture 06, concept 14: Biomolecules need to be solvated (e.g. in water)

Lecture 06, concept 19: Markov state models - slow processes from many short simulations

Lecture 13, concept 02: Full simulations of binding reveal kinetics & barriers

FSDAM vDSSB Non Equilibrium Binding Free Energy | Alchemical Transformations | Protein Ligand System

The Computational Chemist

Lecture 06, concept 10: Flowchart of a typical simulation - femtosecond steps

Lecture 06, concept 02: Molecular dynamics as prediction of motion - challenges

Lecture 06, concept 05: Don't mistake models for reality

Lecture 05, concept 17: Free energy of alpha helix formation

Lecture 06, concept 16: Energy minimisation avoids clashes, which avoids crashes

Lecture 06, concept 13: Examples of systems & timescales to target

Applications of alchemical free energy calculations

Alchemical free energy calculations using pmx

Lecture 06, concept 11: Small fractions of states can still approximate the partition function well