Structural Bioinformatics Tools for Drug Design
Extraction of Biologically Relevant Information from Structural Databases
Article
A Correction to this paper has been published: https://doi.org/10.1186/s13321-021-00528-w
Article
Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity ...
Book
Extraction of Biologically Relevant Information from Structural Databases
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This chapter summarizes the purpose and goals of the book.
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Structural bioinformatics is flourishing from the increased public availability of high-resolution biomacromolecular structures. Careful analysis of these models enables us to study their important structural ...
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The validation of biomacromolecular structures has become a very important topic, because some published structures have been found to contain serious errors. The presence of ligands is a frequent source of er...
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Channels are ligand-accessible pathways inside a biomacromolecular structure. These empty voids inside a structure are composed of the surrounding residues, and as such can be viewed as a form of pattern. Impo...
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Channels are important parts of biomacromolecular structures, because they facilitate the access of ligands to biomacromolecular voids, e.g., active sites, or through a biomacromolecular structure, e.g., trans...
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Structural bioinformatics offers us a way to benefit from the current enormous volume of biological data and use them to increase our understanding of molecular biology, with further applications in protein en...
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This chapter introduces tools for the detection and extraction of biomacromolecular fragments (patterns) of interest from biomacromolecular structures. Afterwards, PatternQuery, a query language for the rigoro...
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provide information about the distribution of electron density within a molecule. Specifically, they reflect the amount of electron density attributed to individual atoms. Information about partial atomic ...
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This chapter provides two bioinformatics projects, which puts all of the above together in a complete and comprehensible package that provides meaningful biological information. The first project focuses on su...
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This chapter contains the solutions to the practical exercises, which are focused on work with databases, the validation of structures, detection and extraction of fragments, detection of channels, characteriz...
Chapter
Nowadays life sciences are filled with data gathered from many sources and these biological data are stored in many databases. Analysis of data gathered within these databases enables new view on the life from...
Article
Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is know...
Article
Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity.