Structural Bioinformatics Tools for Drug Design
Extraction of Biologically Relevant Information from Structural Databases
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Open AccessNEEMP: software for validation, accurate calculation and fast parameterization of EEM charges
The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equal...
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Book
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Chapter
Concluding Remarks
This chapter summarizes the purpose and goals of the book.
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Chapter
Biomacromolecular Fragments and Patterns
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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Chapter
Validation
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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Chapter
Detection of Channels
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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Chapter
Channel Characteristics
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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Chapter
Introduction
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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Chapter
Detection and Extraction of Fragments
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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Chapter
Characterization via Charges
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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Chapter
Complete Process of Data Extraction and Analysis
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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Chapter
Exercises Solution
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...
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Chapter
Structural Bioinformatics Databases of General Use
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...
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Article
Open AccessHigh-quality and universal empirical atomic charges for chemoinformatics applications
Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinform...
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Article
Open AccessAtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules
Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.
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Article
Open AccessQM quality atomic charges for proteins
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Article
Open AccessEmpirical charges for chemoinformatics applications
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Open AccessPredicting pK a values from EEM atomic charges
The acid dissociation constant p K a is a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p K ...
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Article
Open AccessQSPR designer – employ your own descriptors in the automated QSAR modeling process
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Article
Open AccessHow the methodology of 3D structure preparation influences the quality of QSPR models?
