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Table of Contents
Acknowledgement; Contents; Contributors; 1 Introduction; References; Part I Patterns, Fragments and Data Sources; 2 Biomacromolecular Fragments and Patterns; 2.1 Pattern Examples; 2.1.1 Active Site and Their Inhibition
Cyclooxygenase Inhibitors; 2.1.2 Allosteric Site
Structural Flexibility of HIV Protease; 2.1.3 Transcription Factor
Zinc Finger Motif; 2.2 Pattern Prediction; 2.2.1 Ubiquitin-Binding Domain Prediction; 2.2.2 Pattern Detection; 2.2.3 Phosphorylation of Drug Binding Pockets; References; 3 Structural Bioinformatics Databases of General Use
3.1 How a Biomacromolecule Looks Codes What It Does3.2 Worldwide Protein Data Bank (PDB)
Essential Structure Repository; 3.2.1 Protein Data Bank in Europe (PDBe); 3.2.2 RCSB PDB; 3.3 Other Notable Databases; 3.3.1 PDBsum
Pictorial View on PDB Database; 3.3.2 PDB_REDO and WHY_NOT Databases for Curated Structures; 3.3.3 CATH and Pfam Databases for Classification of Protein Folds and Sequences; 3.3.4 PDB Flex, Pocketome and PED3 Databases to Analyze Protein Flexibility and Disorder; 3.3.5 OPM and MemProtMD Databases for Membrane Protein
3.3.6 NDB and GFDB Databases for Other Macromolecules 3.3.7 UniProt and ChEMBL Databases
Power of Connection; 3.4 Conclusion; 3.5 Exercises; 3.5.1 Use of PDBe; 3.5.2 Use of RCSB and ChEMBL; 3.5.3 Use of PDBsum; 3.5.4 Use of CATH; References; 4 Validation; 4.1 Introduction and Motivation; 4.2 Nipah G Attachment Glycoprotein Validation Example; 4.3 Objects of Validation; 4.4 Source Data for Validation; 4.5 Validation Approaches; 4.6 Evolution of Validation Tools; 4.7 How to Handle Structures with Errors; 4.8 Exercises; References; Part II Detection and Extraction
5 Detection and Extraction of Fragments5.1 PatternQuery; 5.1.1 PatternQuery Explained; 5.1.2 Thinking in PatternQuery; 5.1.3 Basic Principles of the Language; 5.2 MetaPocket 2.0; 5.2.1 Serotonin Receptor Example; 5.3 Note on Pattern Comparison; 5.4 Exercises; 5.4.1 PatternQuery; 5.4.2 MetaPocket; References; 6 Detection of Channels; 6.1 Introduction and Motivation; 6.1.1 Bunyavirus Polymerase Example; 6.1.2 Aquaporin Example; 6.2 MOLE
Channel Analysis Tool; 6.3 Identification of Channels Using MOLEonline; 6.3.1 Setup; 6.3.2 Geometry Properties; 6.4 Exercises; References
Part III Characterization7 Characterization via Charges; 7.1 Introduction and Motivation; 7.2 Dinitrotoluene Example; 7.3 Charge Calculation Approaches; 7.4 Charge Visualization; 7.5 Formats for Saving of Charges; 7.6 Exercises; References; 8 Channel Characteristics; 8.1 Physicochemical Properties; 8.1.1 Hydropathy; 8.1.2 Polarity; 8.1.3 Mutability; 8.1.4 Charge; 8.2 Characterization of Channels Using MOLEonline; 8.2.1 Results Analysis; 8.3 Common Errors in Channel Calculation and Characterization; 8.3.1 No Channels Have Been Identified
Cyclooxygenase Inhibitors; 2.1.2 Allosteric Site
Structural Flexibility of HIV Protease; 2.1.3 Transcription Factor
Zinc Finger Motif; 2.2 Pattern Prediction; 2.2.1 Ubiquitin-Binding Domain Prediction; 2.2.2 Pattern Detection; 2.2.3 Phosphorylation of Drug Binding Pockets; References; 3 Structural Bioinformatics Databases of General Use
3.1 How a Biomacromolecule Looks Codes What It Does3.2 Worldwide Protein Data Bank (PDB)
Essential Structure Repository; 3.2.1 Protein Data Bank in Europe (PDBe); 3.2.2 RCSB PDB; 3.3 Other Notable Databases; 3.3.1 PDBsum
Pictorial View on PDB Database; 3.3.2 PDB_REDO and WHY_NOT Databases for Curated Structures; 3.3.3 CATH and Pfam Databases for Classification of Protein Folds and Sequences; 3.3.4 PDB Flex, Pocketome and PED3 Databases to Analyze Protein Flexibility and Disorder; 3.3.5 OPM and MemProtMD Databases for Membrane Protein
3.3.6 NDB and GFDB Databases for Other Macromolecules 3.3.7 UniProt and ChEMBL Databases
Power of Connection; 3.4 Conclusion; 3.5 Exercises; 3.5.1 Use of PDBe; 3.5.2 Use of RCSB and ChEMBL; 3.5.3 Use of PDBsum; 3.5.4 Use of CATH; References; 4 Validation; 4.1 Introduction and Motivation; 4.2 Nipah G Attachment Glycoprotein Validation Example; 4.3 Objects of Validation; 4.4 Source Data for Validation; 4.5 Validation Approaches; 4.6 Evolution of Validation Tools; 4.7 How to Handle Structures with Errors; 4.8 Exercises; References; Part II Detection and Extraction
5 Detection and Extraction of Fragments5.1 PatternQuery; 5.1.1 PatternQuery Explained; 5.1.2 Thinking in PatternQuery; 5.1.3 Basic Principles of the Language; 5.2 MetaPocket 2.0; 5.2.1 Serotonin Receptor Example; 5.3 Note on Pattern Comparison; 5.4 Exercises; 5.4.1 PatternQuery; 5.4.2 MetaPocket; References; 6 Detection of Channels; 6.1 Introduction and Motivation; 6.1.1 Bunyavirus Polymerase Example; 6.1.2 Aquaporin Example; 6.2 MOLE
Channel Analysis Tool; 6.3 Identification of Channels Using MOLEonline; 6.3.1 Setup; 6.3.2 Geometry Properties; 6.4 Exercises; References
Part III Characterization7 Characterization via Charges; 7.1 Introduction and Motivation; 7.2 Dinitrotoluene Example; 7.3 Charge Calculation Approaches; 7.4 Charge Visualization; 7.5 Formats for Saving of Charges; 7.6 Exercises; References; 8 Channel Characteristics; 8.1 Physicochemical Properties; 8.1.1 Hydropathy; 8.1.2 Polarity; 8.1.3 Mutability; 8.1.4 Charge; 8.2 Characterization of Channels Using MOLEonline; 8.2.1 Results Analysis; 8.3 Common Errors in Channel Calculation and Characterization; 8.3.1 No Channels Have Been Identified