Quick Guideline for Computational Drug Design / Sheikh Arslan Sehgal, Rana Adnan Tahir, and Muhammad Waqas.

Format:

Book

Author/Creator:

Sehgal, Sheikh Arslan, author.

Tahir, Rana Adnan, author.

Waqas, Muhammad, author.

Language:

English

Subjects (All):

Drugs--Design.

Drugs.

Physical Description:

1 online resource (126 pages) : illustrations

Edition:

Revised edition.

Place of Publication:

Singapore : Bentham Science Publishers Pte. Ltd., [2021]

Summary:

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. The book provides the reader an easy to read summary of the tools and techniques in structural bioinformatics as well as their limitations. In this revised edition the authors have updated information in a number of chapters with a specific focus on the section on protein structure visualization and evaluation. Additional information on protein-ligand interaction studies has also been provided in this new edition. Therefore the book is a useful handbook for aspiring scholars who wish to learn the basic concepts in computational analysis of biomolecules.

Contents:

Cover

Title

Copyright

End User License Agreement

Contents

Foreword

Preface

CONSENT FOR PUBLICATION

CONFLICT OF INTEREST

ACKNOWLEDGEMENTS

Dedication

Introduction to Structural Bioinformatics

MOTIVATION

BIOINFORMATICS

Bioinformatics Approaches

Static

Dynamic

Structural Bioinformatics

Software and Tools

Open-source Bioinformatics Software

Web Services in Bioinformatics

Virtual Screening

Homology Modeling

Steps of Homology Modeling

Accuracy

Importance of Homology modeling

Homology Modeling Tools

UniProt KB

Structure Prediction Tools

Model Validation Tools

Sequence Analysis Tools

Model Visualization Tools

Virtual Screening and Docking

Recent Advancements in Computational Drug Design

REFERENCES

Protein Primary Sequence Analysis

PROTPARAM EXPASY

Introduction

Brief Instructions

Requirements

Input

Sequence Submission

RESULTS INTERPRETATION

CONCLUSION

LIMITATIONS OF PRIMARY SEQUENCE ANALYSES

ProtParam Expassy

REFERENCE

Secondary Structure Analyses

SECONDARY STRUCTURE OF PROTEINS

PROFUNC

Accessing of Data

LIMITATIONS OF SECONDARY STRUCTURE ANALYSES TOOLS

ProFunc

3D Structure Prediction

STRUCTURE PREDICTION TOOLS

PHYRE2

RESULTS INTERPRETATION (RESULTS SCREEN)

Secondary Structure and Disorder Prediction

Domain Analysis

Detailed Template Information

Alignment View

I-TASSER

Accessing Data

RESULTS INTERPRETATION (OUTPUT)

Structure Prediction.

Top 10 Threading Templates Used by I-TASSER

Top 5 Final Model Predicted by I-TASSER

Structurally Closely Related Protein

Ligand Binding Site

RaptorX

Input Sequence and Domain Partition

Prediction Results

Detailed Prediction Results

SWISS-MODEL

Summary

Templates

Models

3D-JIGSAW

INTFOLD2

HHPRED

M4T

MODELLER

Downloading and Installation

Modeling Steps

Searching for Structures Related to PSEN2

BLAST (BASIC LOCAL ALIGNMENT SEARCHING TOOL)

Template PDB File

Aligning PSEN2 with the Template

Model Building

LIMITATIONS OF STRUCTURE PREDICTION TOOLS

Phyre2

I-Tasser

Swiss-model

3D-Jigsaw

Intfold2

Modeller

Protein 3D Structure Assessment, Evaluation, and Validation

MODEL EVALUATION TOOLS

ERRAT

RESULTS INTERPRETATION (OUTPUT).

CONCLUSION

RAMPAGE

ANOLEA

MOL PROBITY

VERIFY 3D

PDBSUM GENERATE

Output

Customization of Plots

LIMITATIONS OF STRUCTURE EVALUATION TOOLS ERRAT

Rampage

Verify3D

Pdbsum

Ligand-Based Computational Molecular Docking Analysis

INTRODUCTION

Brief Instruction: MOE (Molecular Operating Environment)

Protein-Ligand Interactions

Molecular Operating Environment (MOE)

Protein-Ligand Complex

3D Structure Visualization through MOE

Load and Visualize the Complex

Selection Panel

Protein Active Site and Rendering

Active Site

Rendering

Ribbon Panel

Atoms Panel

Contacts Panel

Fog and ZClip

Molecular Surfaces and Maps

2D Ligand Interaction Diagram

Rendering and Export Image

Subject Index

Back Cover.

Notes:

Includes bibliographical references and index.

Description based on publisher supplied metadata and other sources.

Description based on print version record.

ISBN:

9789814998697

9814998699

OCLC:

1281980622