Structural Bioinformatics Tools for Drug Design [electronic resource] : Extraction of Biologically Relevant Information from Structural Databases /
Koča, Jaroslav.author.
Svobodová Vařeková, Radka.author.
Pravda, Lukáš.author.
Berka, Karel.author.
Geidl, Stanislav.author.
Sehnal, David.author.
Otyepka, Michal.author.
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.
Includes bibliographical references and index.
1. Introduction -- 2. Biomacromolecular fragments  -- 3. Databases -- 4. Detection & Extraction -- a. Biomacromolecular fragments and structural patterns -- b. channels and pores -- 5. Validation -- 6. Characterization -- a. Partial atomic charges -- b. Channel characteristics -- 7. Selected Examples.
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.
Biomedical engineering.
Bioinformatics.
Biomedical Engineering/Biotechnology.
Bioinformatics.
Computational Biology/Bioinformatics.