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Title Structural bioinformatics tools for drug design : extraction of biologically relevant information from structural databases / Jaroslav Koča [and six more].

Published Cham, Switzerland : Springer, [2016]


Location Call No. Status
Physical description 1 online resource.
Series SpringerBriefs in biochemistry and molecular biology
SpringerBriefs in biochemistry and molecular biology.
Springer Biomedical and Life Sciences eBooks 2016 English+International
Bibliography Includes bibliographical references and index.
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
Summary A large amount of structural data on biomacromolecules is available and the number of resolved structures is growing rapidly. This implies that we have an increasing opportunity to perform so far unprecedented analyses to obtain crucial biological insight. Biomacromolecular structural fragments such as binding sites or active sites, ligands, channels, pores, secondary structure motifs, etc., become very promising objects for these analyses because such fragments often serve as drug targets or drug templates, or substrate-specific pathways. However, such analyses are very challenging due to their complexity and, consequently, also because they require application of a combination of different software tools. In this book, we describe individual steps necessary for analysis of biomacromolecular fragments and provide a lsit of software tools required to perform such steps. For each step, we also show corresponding web-based tools in detail and provide a few practical examples of their usage.
Other author Koča, Jaroslav, author.
Vařeková, Radka Svobodová, author.
Pravda, Lukáš, author.
Berka, Karel, author.
Geidl, Stanislav, author.
Sehnal, David, author.
Otyepka, Michal, author.
SpringerLink issuing body.
Subject Structural bioinformatics.
Drugs -- Design.
Electronic books.
Electronic books.
ISBN 9783319473888