Quick Guideline for Computational Drug Design

Bioinformatics allows researchers to answer biological questions with advanced computational methods which involves the application of statistics and mathematical modeling. Structural bioinformatics enables the prediction and analysis of 3D structures of macromolecules while Computer Aided Drug Designing (CADD) assists scientists to design effective active molecules against diseases. However, the concepts in structural bioinformatics and CADD can be complex to understand for students and educated laymen.

This quick guideline is intended as a basic manual for beginner students and instructors involved in bioinformatics and computational chemistry courses. Readers will learn the basics of structural bioinformatics, primary and secondary analysis and prediction, structural visualization, structural analysis and molecular docking. Therefore, the book is a useful handbook for aspiring scholars who wish to learn the basic concepts in computational analysis of biomolecules.

Preface:

The discussion of the bulk amount of informational data in biological sciences is still an understatement. The bioinformatics studies are being practiced in all over the world by universities, scientific groups, international and national companies and consortia, and it would not be underestimating if bioinformatics will be thought of as bedrock of future biological sciences. Bioinformatics evolved into complete interdisciplinary science to solve the biological problems by utilizing statistical, mathematical and computational approaches. Furthermore, the recording, annotation, storage, analyses, and searching/retrieval of biological information and representing this concluded information in order to understand various pathways, to educate ourselves, to understand biological processes in disease and healthy states, and also find potential drugs are only some aspects of bioinformatics. The conjuring of new ‘Big-Data’ associated typically with enormous databases of protein/gene sequences, and functional/structural information into which novel proteins and genes sequences are constantly deposited, can easily be searched by remote computer access with already known sequences. Numerous bioinformatics tools are freely available on the Internet to whoever wants to utilize them and it is impossible to list them all. The ability to collect, save, annotate, analyze, and distributes the biological information retrieved from sequencing and functional analyses is significant for modern biology. This is the reason behind the wide spread belief that the long run significance of bioinformatics approaches lies not much in the available tools, but in the annotation of data and concluding logical information that bioinformatics delivers for the improvement of life sciences.

Bioinformatics is to solve the biological problems with advanced computational manners by applying statistical and mathematical approaches. Structural bioinformatics is to predict and analyze 3D structures of macromolecules while Computer aided drug designing (CADD) helps scientists to design effective active molecules against diseases. However, the concept of structural bioinformatics including CADD is still hard to grasp for students and even more for educated laymen.

With this book, we attempt to show the step by step working of basic tools for drug designing wherein analyses of generated results is always a priority. The protein sequence of RASSF2 was retrieved from UniProt and primary sequence analyses, secondary structure prediction and 3D structure prediction was performed followed by molecular docking studies. The basic information about bioinformatics and utilized tools is summarized in the first chapter. The book is summarized just as we wish we had been taught the core concepts and the working when we were first introduced to it. Therefore, we hope that it can be helpful as a guideline for drug designing by in silico approaches. The main text of the present work aims to demonstrate the step by step visual demonstration of the basic tools of structural bioinformatics and also is focused on the scientific point of views. If a beginner retrieves a protein sequence and performed all the steps described visually in this book will not only learn the computational drug designing but also can generate a publishable data.