Quick guideline for computational drug design (Revised Edition) / / authored by Sheikh Arslan Sehgal, Rana Adnan Tahir, and Muhammad Waqas

• Record Nr.: UNINA9910825102403321
• Autore: Sehgal Sheikh Arslan
• Pubbl/distr/stampa: Singapore : , : Bentham Science Publishers, , 2021; ©2021
• ISBN: 981-4998-69-9
• Edizione: [Revised edition]
• Descrizione fisica: 1 online resource (126 pages) : illustrations
• Altri autori (Persone): TahirRana Adnan; WaqasMuhammad
• Soggetti: Drug Design; Computer-Aided Design
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: 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.