Glossary

B-Factor

B-Factor, also called "Temperature factor" is a correction term used in the analysis of the electron density data obtained from X-ray crystallography, that compensates the smear of the density caused by changes in the atom position in the crystal. Molecular dynamics can reproduce such movements, and hence B-factor applied to molecular dynamics trajectories is an indication of the fluctuation of atoms around their equilibrium positions.

Backbone

The backbone or main chain of a protein is constituted by CO, NH and Cα atoms. It forms the skeleton where aminoacid side chains are attached, and determines the fold of the protein molecule. The backbone is responsible of the main changes in the conformation of the protein.

Cutoff radius

Maximum distance for the pairs of atoms to be included in the calculation.

Lindemann

The Lindemann coefficient is a measure of the viscosity behaviour of the protein. Higher numbers corresponds to liquid-like behaviour, while lower numbers are related to more solid-like behaviour.

MoDEL

Molecular Dinamics Extended Library is a library of molecular dynamics trajectories and their corresponding analysis.

PC

Each of the eigenvector obtained from Principal Component Analysis of a trajectory is called a principal component (PC). The associated eigenvalue indicates the amount of variance explained by the component.

PCA

Principal Component Analysis (PCA) is a transformation of a data set to a new vector basis whose components are ordered according to the amount of variance explained. This approach helps to reduce the dimensionality of the data, and makes easier to analyze the main components of the movement of the structures being studied. PCA analysis applied to trajectories is performed by diagonalization of the correlation matrix.

PCZ

Principal Components Zip (PCZ) files are molecular trajectories compressed using the Principal Component Analysis techniques. This file format can be processed with the PCASuite suite of tools.

PDB

PDB stands for Protein Data Bank (https://www.pdb.org). PDB is the major public repository of three dimensional structures of macromolecules. PDB format corresponds to a the original file format used by PDB, that has been adopted as a standard for representing macromolecular structures.

PDB File Format - Contents Guide Version 3.2 (September 15, 2008)

Requested accuracy

In PCZ format, this term is the percentage of the variance that will be taken into account when selecting how many eigenvectors include in the compressed trajectory. Higher values give a better fidelity to the original trajectory, but lead to poorer compression factors. The default value used in FlexServ is 90%.

Sidechain

The protein sidechains are the atoms that does not belong to the backbone. Each aminoacid have a different sidechain, which gives the aminoacid its properties.

Size of essential space

In Principal Component Analysis, this is the number of eigenvalues above 1 Å2.

Temperature

The temperature is proportional to the kinetic energy of the particles, that is proportional to the particle velocity squared. In molecular simulations the temperature is used to define the average velocities of the particles being simulated. Therefore higher temperatures imply faster particle movements.