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.
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.
Brownian Dynamics is a molecular simulation method in which the temperature is kept constant by a stochastic bath. This can be done by considering a velocity-dependent friction force and a white Robust random term in the Newton equations.
The collectivity index gives a measure of how many atoms of the protein are affected by a Principal Component.
The correlation coefficient applied to protein dynamics shows the relationship between the movements of two given protein residues.
Maximum distance for the pairs of atoms to be included in the calculation.
In Principal Component Analysis, the dimensionality defines how many ortogonal movements define a given threshold of variance.
In Discrete Molecular Dynamics, proteins are modeled as a system of beads (representing Cα atoms) interacting through a discontinuous potential (square wells). Outside the discontinuites, particles move in a constant potential region, therefore in ballistic regime (constant velocities).
In Brownian Dynamics simulations, Δt is the time ellapsed between two consecutive time steps.
Measure of the strength of the spring connecting atoms measured in Kcal/mol·Å².
A hinge point is a position in the protein backbone where the protein bends. Major domain movements in proteins occur through hinge points
In Normal Mode Analysis, the Kovacs algorithm uses a distance-dependent potential.
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.
In Normal Mode Analysis, the Linear algorithm uses a unique potential is used for all interactions considered.
In Normal Mode Analysis, the Mixed algorithm uses a potentials adjusted to atomistic MD simulations.
Molecular Dinamics Extended Library is a library of molecular dynamics trajectories and their corresponding analysis.
Normal Mode Analysis is a classical technique for studying the vibrational properties of atomic structures. Here, the topology of the molecule is defined by a network of springs which includes all the interactions or the ones within a given cutoff distance.
In Brownian Dynamics simulations, this parameter is the number of frames after which a frame is written and considered for analysis.
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.
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.
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 stands for Protein Data Bank (http://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)
In Brownian Dynamics simulations, it is the mean distance between consecutive Cα atoms.
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%.
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.
In Discrete Molecular Dynamics, Sigma is the well amplitude for consecutive Cα atoms.
In Discrete Molecular Dynamics, "Sigma Go" is the well amplitude for non-consecutive Cα.
In Principal Component Analysis, this is the number of eigenvalues above 1 Å2.
In Brownian Dynamics simulations, the number of time steps that will be performed during the simulation.
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.