Title:Overview of Free Software Developed for Designing Drugs Based on Protein-Small Molecules Interaction
Volume: 18
Issue: 13
Author(s): Piyush Agrawal, Pawan Kumar Raghav, Sherry Bhalla, Neelam Sharma and Gajendra P.S. Raghava*
Affiliation:
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi,India
Keywords:
Protein-small molecule interaction, Structure Prediction, Docking, Pharmacophore, Molecular Dynamics, Post
Translational Modifications.
Abstract: One of the fundamental challenges in designing drug molecule against a disease target or protein
is to predict binding affinity between target and drug or small molecule. In this review, our focus
will be on advancement in the field of protein-small molecule interaction. This review has been divided
into 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. In
the second section, we will discuss software packages developed for predicting small-molecule interacting
residues in a protein. Advances in the field of docking particularly advancement in the knowledgebased
force fields will be discussed in the third part of the review. This section will also cover the
method developed for predicting affinity between protein and drug molecules. The fourth section of the
review will describe miscellaneous techniques used for designing drug molecules, like pharmacophore
modelling. Our major emphasis in this review will be on computational tools that are available free for
academic use.
