Overview of Free Software Developed for Designing Drugs Based on Protein-Small Molecules Interaction

Publisher: Bentham Science Publishers

E-ISSN: 1873-4294|18|13|1146-1167

ISSN: 1568-0266

Source: Current Topics in Medicinal Chemistry, Vol.18, Iss.13, 2018-05, pp. : 1146-1167

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Abstract

One of the fundamental challenges in designing drug molecule against a disease target or proteinis to predict binding affinity between target and drug or small molecule. In this review, our focuswill be on advancement in the field of protein-small molecule interaction. This review has been dividedinto four major sections. In the first section, we will cover software developed for protein structure prediction.This will include prediction of binding pockets and post-translation modifications in proteins. Inthe second section, we will discuss software packages developed for predicting small-molecule interactingresidues in a protein. Advances in the field of docking particularly advancement in the knowledgebasedforce fields will be discussed in the third part of the review. This section will also cover themethod developed for predicting affinity between protein and drug molecules. The fourth section of thereview will describe miscellaneous techniques used for designing drug molecules, like pharmacophoremodelling. Our major emphasis in this review will be on computational tools that are available free foracademic use.