The Resource Structural bioinformatics tools for drug design : extraction of biologically relevant information from structural databases, Jaroslav Koča [and six more]

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

Label
Structural bioinformatics tools for drug design : extraction of biologically relevant information from structural databases
Title
Structural bioinformatics tools for drug design
Title remainder
extraction of biologically relevant information from structural databases
Statement of responsibility
Jaroslav Koča [and six more]
Contributor
Author
Subject
Genre
Language
eng
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
Member of
Cataloging source
N$T
Dewey number
572/.330285
Index
index present
LC call number
QH324.2
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
http://library.link/vocab/relatedWorkOrContributorName
  • Koča, Jaroslav
  • Vařeková, Radka Svobodová
  • Pravda, Lukáš
  • Berka, Karel
  • Geidl, Stanislav
  • Sehnal, David
  • Otyepka, Michal
Series statement
SpringerBriefs in biochemistry and molecular biology
http://library.link/vocab/subjectName
  • Structural bioinformatics
  • Drugs
  • SCIENCE
  • Drugs
  • Structural bioinformatics
  • Biomedicine
  • Biomedical Engineering/Biotechnology
  • Bioinformatics
  • Computational Biology/Bioinformatics
Label
Structural bioinformatics tools for drug design : extraction of biologically relevant information from structural databases, Jaroslav Koča [and six more]
Link
https://ezproxy.lib.ou.edu/login?url=http://link.springer.com/10.1007/978-3-319-47388-8
Instantiates
Publication
Antecedent source
unknown
Bibliography note
Includes bibliographical references and index
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier
Color
multicolored
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
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
Dimensions
unknown
Extent
1 online resource.
File format
unknown
Form of item
online
Isbn
9783319473888
Level of compression
unknown
Media category
computer
Media MARC source
rdamedia
Media type code
  • c
Note
SpringerLink
Other control number
10.1007/978-3-319-47388-8
Quality assurance targets
not applicable
Reformatting quality
unknown
Sound
unknown sound
Specific material designation
remote
System control number
  • (OCoLC)970041816
  • (OCoLC)ocn970041816
Label
Structural bioinformatics tools for drug design : extraction of biologically relevant information from structural databases, Jaroslav Koča [and six more]
Link
https://ezproxy.lib.ou.edu/login?url=http://link.springer.com/10.1007/978-3-319-47388-8
Publication
Antecedent source
unknown
Bibliography note
Includes bibliographical references and index
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier
Color
multicolored
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
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
Dimensions
unknown
Extent
1 online resource.
File format
unknown
Form of item
online
Isbn
9783319473888
Level of compression
unknown
Media category
computer
Media MARC source
rdamedia
Media type code
  • c
Note
SpringerLink
Other control number
10.1007/978-3-319-47388-8
Quality assurance targets
not applicable
Reformatting quality
unknown
Sound
unknown sound
Specific material designation
remote
System control number
  • (OCoLC)970041816
  • (OCoLC)ocn970041816

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