Basics, types and applications of molecular docking: A review

Abstract

From hit discovery through lead optimization and beyond, computational methods have become an essential part of many drugs development processes. There are typically several steps in the docking process, and each one provides a new level of complexity. Docking methods are used to place small molecules in the active region of the enzyme. In addition to these methods, scoring functions are used to estimate a compound's biological activity by looking at how it interacts with prospective targets. Molecular docking is considered to be the most widely utilized computational phenomenon in the field of computer-aided drug design (CADD). It is being utilized at the academic level as well as in pharmaceutical companies for the lead discovery process. Molecular docking is mainly associated with two terms: ligand and protein. Protein is the target site where ligand may bind to give specific activity. Molecular docking provides information on the ability of the ligand to bind with protein which is known as binding affinity. Applications of molecular docking in drug development have evolved significantly since it was first created to aid in the study of molecular recognition processes between small and large compounds. This review emphasizes the basic features of molecular docking along with the types, approaches and applications.

Manganese Schiff Base Complexes, Crystallographic Studies, Anticancer Activities, and Molecular Docking

“…In line with Müller, among the six researchers who studied crystallography of Mn(II) and Mn(III) complexes, Bermejo et [75,[78][79][80]. Müller further stated that crystal structure could be determined at more than one temperature, because occasionally the crystal packing varies as a function of temperature, and this variation is seldom accompanied by noticeable crystal cracking [86]. In line with Müller's further statement, none of the six crystallographic studies reported using more than one temperature [75,[78][79][80][81][82]87].…”

“…Computational approach through molecular docking coupled with searching and scoring is one of the most significant approaches for drug design and discovery, which allows molecular interactions and prediction between a ligand and the receptor in the bound state. e two types of docking are protein-protein docking and ligand-protein docking [86].…”

Selecting antibacterial aptamers against the BamA protein in Pseudomonas aeruginosa by incorporating genetic algorithm to optimise computational screening method

“…Molecular docking is often employed to characterise and simulate the binding affinities and structural properties of complexes, a common practice prior to in vitro experiments, thus saving time and labour. Hence, drug design studies favour docking simulations, and several algorithms have been developed since, such as HADDOCK, ZDOCK, HDock, AutoDock, AutoDock Vina, Rosetta and many more 18 , 19 . However, a few studies have advised that further work is required to analyse the binding complexes, despite finding their respective best structure 20 .…”

Synthesis, Biological Evaluation andin SilicoStudies of 3‐Hydroxy‐N‐(2‐(substituted phenyl)‐4‐oxothiazolidin‐3‐yl)‐2‐napthamide Derivatives

“…They act as antibacterial, [12–22] antifungal, [15–22] anti‐inflammatory, [22–24] antidiabetic agents, [23,36] anti‐oxidant, [13,14,22,26–28] genotoxicity, [12,32] cytotoxicity, [30,32] anticancer, [25,31,32] anticonvulsant, [24,27,31] antiviral activity, [34] antitubercular, [35] analgesic, [22,23] and antidiabetic agents [23,36] . The examination, interpretation, explanation, and discovery of molecular characteristics using three‐dimensional structures are made easier with the help of the low‐cost, safe, and straightforward process known as molecular docking [37] . Numerous molecular modelling methodology have been authoritatively used in drug development by pharmaceutical researchers/Scientists.…”

“…[23,36] The examination, interpretation, explanation, and discovery of molecular characteristics using three-dimensional structures are made easier with the help of the low-cost, safe, and straightforward process known as molecular docking. [37] Numerous molecular modelling methodology have been authoritatively used in drug development by pharmaceutical researchers/ Scientists. Docking has developed a more decisive tool in pharmaceutical research as a repercussion of programmes established on disparate algorithms being inaugurated to undertake molecular docking studies.…”