Molecular Docking: Approaches, Types, Applications and Basic Challenges

Abstract

Molecular docking is a kind of bioinformatic modelling which involves the interaction of two or more molecules to give the stable adduct. Depending upon binding properties of ligand and target, it predicts the three-dimensional structure of any complex. Molecular docking generates different possible adduct structures that are ranked and grouped together using scoring function in the software. Docking simulations predict optimized docked conformer based upon total energy of the system. In spite of all potential approaches, ligand chemistry (tautomerism and ionization), receptor flexibility (single conformation of rigid receptor) and scoring function (differentiate true binding mode) still remained the challenge. Many important aspects of molecular docking in terms of its approaches, types, applications and challenges are briefly discussed in this article.

Thrombolytic Activity, Drug Likeness Property and ADME/T Analysis of Isolated Phytochemicals from Ginger (<i>Zingiber officinale</i>) Using <i>In Silico</i> Approaches

“…In silico ADME/T predictive tools are designed to assist in vivo/in vitro toxicological and pharmacological profiling of pharmaceutical compounds which in turn enables a better understanding of drug safety and liabilities. But less accuracy and low sensitivity sometimes may lead to faulty predictions also [16] [37] [38].…”

Synthesis of New Derivatives of 1,2,3‐Triazole‐Linked Phthalazine‐1,4‐dione in Water: Experimental Aspects and Molecular Docking Calculations

“…It is a tool for prediction and recognition of ligand‐macromolecule complex interactions for the rational discovery and design of drugs. It is also applied in the mechanistic study by placing a molecule into the preferred active site of the specific target region of proteins . Docking can be accomplished through two interrelated steps: first by sampling conformations of the ligands in the active sites of proteins; then ranking these conformations via a scoring function …”

Docking Studies on Novel Analogues of 8-Chloro-Quinolones against Staphylococcus aureus

“…An important parameter in the development of a new drug is the drug's affinity to the identified target (protein/enzyme). Predicting the ligand binding to the target (protein/enzyme) by molecular simulation would allow the synthesis to be restricted to the most promising compounds [1][2][3][4][5][6][7][8][9]. Molecular docking can be accomplished by two interdependent steps [7][8][9].…”