README.md

• Apo structure
• Conformation
• Holo structure
• Orientation
• Pose
• Root-mean-square deviation(RMSD)

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Apo structure

The observed structure of a protein if its ligand is not bound. In contrast to holo structure

Conformation

• Ligands/proteins can exist in different conformations. Usually, "conformation" refers to the same chemical composition but with altered bond-angles between two/multiple ligands or proteins. See also orientation.

Holo structure

The observed structure of a protein in its ligand bound state. In contrast to apo structure

Orientation

• In contrast to conformation, the bond angles are the same between two/multiple ligands (as well as the chemical composition), but the orientation in space (transition, global rotation) is differs between two/multiple orientations.

Pose

A ligand pose describes the binding-mode of a ligand in a protein binding site. Typically, this is considered to be a combination of orientation & conformation

Root-mean-square deviation (RMSD)

The RMSD measures the average distance between atoms of 2 protein or ligand structures via the equation

where a_i refers to the atoms of molecule 1, and b_i to the atoms of molecule 2, respectively. The subscripts x, y, z are denoting the x-y-z coordinates for every atom.

The RMSD is most commonly calculated without taking hydrogen-atoms into consideration (typically only C-alpha or main-chain atoms in proteins).

(overlay between 2 ligand structures, RMSD = 1.9959 Angstrom)