Quick Guideline for Computational Drug Design (Revised Edition).

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
MOTIVATION
PROTPARAM EXPASY
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
RESULTS INTERPRETATION
CONCLUSION
LIMITATIONS OF PRIMARY SEQUENCE ANALYSES
ProtParam Expassy
REFERENCE
Secondary Structure Analyses
MOTIVATION
SECONDARY STRUCTURE OF PROTEINS
PROFUNC
Brief Instructions
Requirements
Input
Sequence Submission
Accessing of Data
LIMITATIONS OF SECONDARY STRUCTURE ANALYSES TOOLS
ProFunc
REFERENCES
3D Structure Prediction
MOTIVATION
STRUCTURE PREDICTION TOOLS
PHYRE2
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
RESULTS INTERPRETATION (RESULTS SCREEN)
Secondary Structure and Disorder Prediction
Domain Analysis
Detailed Template Information
Alignment View
CONCLUSION
I-TASSER
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
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
CONCLUSION
RaptorX
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
Accessing Data
RESULTS INTERPRETATION (OUTPUT)
Input Sequence and Domain Partition
Prediction Results
Detailed Prediction Results
SWISS-MODEL
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
RESULTS INTERPRETATION (RESULTS SCREEN)
Summary
Templates
Models
CONCLUSION
3D-JIGSAW
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
Accessing Data
RESULTS INTERPRETATION
CONCLUSION
INTFOLD2
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
Accessing Data
RESULTS INTERPRETATION (OUTPUT)
CONCLUSION
HHPRED
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
Accessing Data
RESULTS INTERPRETATION (OUTPUT)
CONCLUSION
M4T
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
Accessing Data
RESULTS INTERPRETATION (OUTPUT)
CONCLUSION
MODELLER
Introduction
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
RaptorX
Swiss-model
3D-Jigsaw
Intfold2
M4T
Modeller
REFERENCES
Protein 3D Structure Assessment, Evaluation, and Validation
MOTIVATION
MODEL EVALUATION TOOLS
ERRAT
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
RESULTS INTERPRETATION (OUTPUT).

CONCLUSION
RAMPAGE
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
RESULTS INTERPRETATION
CONCLUSION
ANOLEA
Introduction
Brief Instructions
Requirements
Input
RESULTS INTERPRETATION
CONCLUSION
MOL PROBITY
Introduction
Brief Instructions
Requirements
Input
RESULTS INTERPRETATION
CONCLUSION
VERIFY 3D
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
RESULTS INTERPRETATION
CONCLUSION
PDBSUM GENERATE
Introduction
Brief Instructions
Requirements
Input
Sequence Submission
Accessing Data
RESULTS INTERPRETATION
Output
Customization of Plots
LIMITATIONS OF STRUCTURE EVALUATION TOOLS ERRAT
Rampage
Verify3D
Pdbsum
REFERENCES
Ligand-Based Computational Molecular Docking Analysis
INTRODUCTION
Brief Instruction: MOE (Molecular Operating Environment)
REFERENCES
Protein-Ligand Interactions
MOTIVATION
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
REFERENCE
Subject Index
Back Cover.