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000775371 019__ $$a970635903
000775371 020__ $$a9783319473888$$q(electronic book)
000775371 020__ $$a3319473883$$q(electronic book)
000775371 020__ $$z9783319473871
000775371 035__ $$aSP(OCoLC)ocn970041816
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000775371 049__ $$aISEA
000775371 050_4 $$aQH324.2
000775371 08204 $$a572/.330285$$223
000775371 24500 $$aStructural bioinformatics tools for drug design :$$bextraction of biologically relevant information from structural databases /$$cJaroslav Koča [and six more].
000775371 264_1 $$aCham, Switzerland :$$bSpringer,$$c[2016]
000775371 300__ $$a1 online resource.
000775371 336__ $$atext$$btxt$$2rdacontent
000775371 337__ $$acomputer$$bc$$2rdamedia
000775371 338__ $$aonline resource$$bcr$$2rdacarrier
000775371 4901_ $$aSpringerBriefs in biochemistry and molecular biology
000775371 504__ $$aIncludes bibliographical references and index.
000775371 5050_ $$aAcknowledgement; 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
000775371 5058_ $$a3.1 How a Biomacromolecule Looks Codes What It Does3.2 Worldwide Protein Data Bank (PDB) -- Essential Structure Repository; 3.2.1 Protein Data Bank in Europe (PDBe); 3.2.2 RCSB PDB; 3.3 Other Notable Databases; 3.3.1 PDBsum -- Pictorial View on PDB Database; 3.3.2 PDB_REDO and WHY_NOT Databases for Curated Structures; 3.3.3 CATH and Pfam Databases for Classification of Protein Folds and Sequences; 3.3.4 PDB Flex, Pocketome and PED3 Databases to Analyze Protein Flexibility and Disorder; 3.3.5 OPM and MemProtMD Databases for Membrane Protein
000775371 5058_ $$a3.3.6 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
000775371 5058_ $$a5 Detection and Extraction of Fragments5.1 PatternQuery; 5.1.1 PatternQuery Explained; 5.1.2 Thinking in PatternQuery; 5.1.3 Basic Principles of the Language; 5.2 MetaPocket 2.0; 5.2.1 Serotonin Receptor Example; 5.3 Note on Pattern Comparison; 5.4 Exercises; 5.4.1 PatternQuery; 5.4.2 MetaPocket; References; 6 Detection of Channels; 6.1 Introduction and Motivation; 6.1.1 Bunyavirus Polymerase Example; 6.1.2 Aquaporin Example; 6.2 MOLE -- Channel Analysis Tool; 6.3 Identification of Channels Using MOLEonline; 6.3.1 Setup; 6.3.2 Geometry Properties; 6.4 Exercises; References
000775371 5058_ $$aPart 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
000775371 506__ $$aAccess limited to authorized users.
000775371 520__ $$aA 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.
000775371 588__ $$aOnline resource; title from PDF title page (SpringerLink, viewed February 3, 2017).
000775371 650_0 $$aStructural bioinformatics.
000775371 650_0 $$aDrugs$$xDesign.
000775371 7001_ $$aKoča, Jaroslav,$$eauthor.
000775371 7001_ $$aVařeková, Radka Svobodová,$$eauthor.
000775371 7001_ $$aPravda, Lukáš,$$eauthor.
000775371 7001_ $$aBerka, Karel,$$eauthor.
000775371 7001_ $$aGeidl, Stanislav,$$eauthor.
000775371 7001_ $$aSehnal, David,$$eauthor.
000775371 7001_ $$aOtyepka, Michal,$$eauthor.
000775371 77608 $$iPrint version:$$aKoča, Jaroslav$$tStructural Bioinformatics Tools for Drug Design : Extraction of Biologically Relevant Information from Structural Databases$$dCham : Springer International Publishing,c2016$$z9783319473871
000775371 830_0 $$aSpringerBriefs in biochemistry and molecular biology.
000775371 852__ $$bebk
000775371 85640 $$3SpringerLink$$uhttps://univsouthin.idm.oclc.org/login?url=http://link.springer.com/10.1007/978-3-319-47388-8$$zOnline Access$$91397441.1
000775371 909CO $$ooai:library.usi.edu:775371$$pGLOBAL_SET
000775371 980__ $$aEBOOK
000775371 980__ $$aBIB
000775371 982__ $$aEbook
000775371 983__ $$aOnline
000775371 994__ $$a92$$bISE