25 Result(s)
within
Chapter
Karel Berka
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Chapter
Concluding Remarks
This chapter summarizes the purpose and goals of the book.
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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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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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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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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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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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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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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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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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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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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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Rational and Nonrational Elements in the History of Science
It is the aim of my contribution to analyze the relevance of nonrational elements in the history of science, more exactly the dialectics of scientific and unscientific roots of modern science. As a prerequisit...
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The Ideal of Mathematization in B. Bolzano
In my contribution I would like to draw attention to the views on the ideal of mathematization held by B. Bolzano, a later follower of Leibnizian rationalism. This analysis will show the evolution of conceptio...
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Introduction
Measurement is a quite common procedure in the everyday practice of human-kind and each individual. Measurement and counting — operations directly connected with the material life of society — have developed i...
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Quantification
After having exposed the concepts of measurement, magnitude, and scale, there still remains the task of considering the content and extension of the concept of quantification. In the explication of this concep...
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Philosophical Problems of Measurement
The elucidation of basic notions, the investigation of empirical and mathematical components of measurement, the analysis of its formal characteristics, as well as the practical application of measuring proced...
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Measurement
The concept of measurement, as it is understood in the most diverse connections, often with different intentions, is undoubtedly a complex concept possessing an equivocal meaning. We have already pointed this ...
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Scales
The differentiation of metrical and non-metrical magnitudes on the empirico-mathematical level of the conceptualization of the object of measurement must necessarily appear in an explication of the result of m...
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Theory of Measurement
One can speak of a theory of measurement in various connections. This situation is caused not only by our peculiar ways of interpreting the concept of measurement (we might interpret it in a wider or a narrowe...
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Methodological Problems of Measurement
There is a whole range of general and specific problems of a methodological character that are connected with measurement. The selection of these problems undoubtedly depends on the level of generality and the...
