Difference Between Molecular Docking and Scoring

The key difference between molecular docking and scoring is that docking is a technique used to determine the binding affinity between two molecules whereas scoring is a process of evaluating a particular pose by counting the number of favourable intermolecular interactions.

The terms molecular docking and scoring are used in the field of molecular modelling. Molecular modelling is a technique used to determine the possible arrangements of different molecules in a given substance. This technique is important in creating new stable compounds.

CONTENTS

1. Overview and Key Difference
2. What is Molecular Docking
3. What is Molecular Scoring
4. Side by Side Comparison – Molecular Docking vs Scoring in Tabular Form
5. Summary

What is Molecular Docking?

Molecular docking is a computational simulation of a candidate ligand binding to a receptor. This method predicts the preferred orientation of one molecule to another molecule when bound to each other to form a stable complex. The results obtained from this technique can be used to predict the strength of association or binding affinity between two molecules. Here, the molecular scoring function is also important.

Generally, this technique considers the biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids. These molecules are very important, and they play an important role in signal transduction mechanisms in our body. Therefore, the orientation of the two molecules that are going to bind for this signal transduction process affects the type of signal produced here. That means; molecular docking is important in determining both the strength and the type of signal produced during signal transduction in biological systems.

Moreover, molecular docking techniques are important in designing structure-based drugs. That is due to its predictability of binding conformation of small molecules such as ligands to a suitable binding site.

What is Molecular Scoring?

Molecular scoring is a type of mathematic function that is useful in evaluating the progress of molecular docking. In the field of computational chemistry, scoring functions are used for predicting the binding affinity between two molecules after the process of docking. For example, if we have a small molecule of a particle drug and there is a biological target such as a protein, we can evaluate the affinity of the drug towards the binding site. Moreover, the molecular scoring can be used to predict the intermolecular interactions between two proteins or between a protein and DNA molecules.

The major application of molecular scoring is in the drug designing processes—for example, virtual screening, de novo designing, lead optimization, etc.

What is the Difference Between Molecular Docking and Scoring?

Molecular docking and scoring are important in molecular modelling. The key difference between molecular docking and scoring is that docking is a technique used to determine the binding affinity between two molecules whereas scoring is a process of evaluating a particular pose by counting the number of favourable intermolecular interactions.

The following infographic summarizes the difference between molecular docking and scoring.

Summary – Molecular Docking vs Scoring

Molecular docking and scoring are important in molecular modelling. The key difference between molecular docking and scoring is that docking is a technique used to determine the binding affinity between two molecules whereas scoring is a process of evaluating a particular pose by counting the number of favourable intermolecular interactions.

Reference:

1. “Docking (Molecular).” Docking (Molecular) – an Overview | ScienceDirect Topics, Available here.
2. Dar, Ayaz Mahmood. “Molecular Docking: Approaches, Types, Applications and Basic Challenges.” OMICS International, OMICS International, 27 Mar. 2017, Available here.

Image Courtesy:

1. “Docking representation 2” By Scigenis – Own work (CC BY-SA 4.0) via Commons Wikimedia
2. “Scoringfunction” By Poulamibarman at English Wikibooks – Transferred from en.wikibooks to Commons by Adrignola using CommonsHelper (Public Domain) via Commons Wikimedia