06686nam 22004933 450 991082510240332120230627185435.0981-4998-69-9(CKB)4950000000281275(MiAaPQ)EBC6748487(Au-PeEL)EBL6748487(OCoLC)1281980622(EXLCZ)99495000000028127520211214d2021 uy 0engurcnu||||||||txtrdacontentcrdamediacrrdacarrierQuick guideline for computational drug design (Revised Edition) /authored by Sheikh Arslan Sehgal, Rana Adnan Tahir, and Muhammad WaqasRevised editionSingapore :Bentham Science Publishers,2021.©2021.1 online resource (126 pages) illustrations981-4998-70-2 Includes bibliographical references and index.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.Quick Guideline for Computational Drug DesignDrug DesignComputer-Aided DesignDrug Design.Computer-Aided Design.Sehgal Sheikh Arslan1624493Tahir Rana Adnan1624494Waqas Muhammad1624495MiAaPQMiAaPQMiAaPQBOOK9910825102403321Quick guideline for computational drug design (Revised Edition)3959489UNINA