Description
The book describes the individual steps necessary for biomacromolecular fragments analysis, as well as a list of essential software tools. For each step, it also shows corresponding web-based tools in detail and provides practical examples of their use. All tools and databases mentioned in the examples are available free of charge, platform-independent, web-based, user-friendly and do not require a prior IT background to be fully used. Prof. RNDr. Jaroslav Koca, DrSc., is director of the Central European Institute of Technology and Head of the research group Computational Chemistry at Masaryk University in Brno, Czech Republic. His field of expertise is mathematical and computer assisted chemistry and biochemistry, computer assisted molecular modeling of biologically interesting chemical species, information technology in chemistry, biochemistry, and environmental chemistry. Last years projects were mainly on conformational search, molecular docking and molecular dynamics simulations on peptides, proteins, oligonucleotides, nucleotide sugars, and carbohydrates. Methods for analysis conformational potential energy surfaces and energy landscapes of chemical reactions using molecular mechanics and quantum chemistry techniques. For more information see: http://www.chemi.muni.cz/~jkoca/ 1. Introduction Description of current situation about biomacromolecular structural data, their amount, growth, availability. Motivation, why it has sense to process and analyze these data, including applications towards drug design. Description of basic steps of their analysis via structural bioinformatics approaches. 2. Biomacromolecular fragments 3. Databases Status of current structural databases focused on biomacromolecules, ligands, fragments, structural patterns etc. Practical examples based on PDBe and PDBsum. 4. Detection & Extraction Languages and formalisms for description, detection, extraction and comparison of biomacromolecular fragments and structural patterns. Practical examples based on PatternQuery and SiteBinder. Approaches and software tools for extraction of channels and pores. Practical examples based on MOLE. 5. Validation Methodologies and software tools for validation of biomacromolecules and ligands. Practical examples based on MotiveValidator, ValidatorDB and PDBe validation reports. 6. Characterization Calculation of partial atomic charges of biomacromolecules and ligands. Practical examples based on AtomicChargeCalculator. Calculation of channel characteristics (radius, length, lining residues, physico-chemical properties). Practical examples based on MOLE. 7. Selected Examples > fragment(s) definition -> database search and data extraction -> data validation -> atomic charges calculation/biomacromolecular channel ^ conclusions.
