Carboxypeptidase A – Computational Studies

Synonyms

NEB (nudged elastic band); Self-Consistent Charge Density Function Tight Binding (SCC-DFTB)

Definition

Quantum Mechanics (QM) methods describe the electronic structure of molecules by solving the Schrödinger equation.

Molecular Mechanics (MM) methods describe the molecular structure without explicit description of electrons, using an empirical force field.

QM/MM methods combine a quantum mechanical method to characterize the active site of a molecular (e.g., enzyme) system with a molecular mechanical method to characterize the remaining part of the system.

An all-atom force field is a molecular mechanics potential function, i.e., a set of parameters and functions to determine the potential energy of a molecular system, in which all atoms are treated explicitly.

A “cluster model” is a truncated model of a large molecular system where only the most relevant atoms of the system under study (e.g., catalytic residues, substrate, cofactors) are included in the calculation.

Biological...