Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases

ISBN-13: 9783319473871 / Angielski / Miękka / 2017 / 144 str.

Jaroslav Ko a.; Radka Svobodova Va Ekova; Luka Pravda

Opis

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.

Spis treści

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

1. Languages and formalisms for description, detection, extraction and comparison of biomacromolecular fragments and structural patterns. Practical examples based on PatternQuery and SiteBinder.

2. 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

1. 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

Few biologically relevant examples where all or most of the tools would be used. Small exemplary bioinformatics project. Problem formulation -> fragment(s) definition -> database search and data extraction -> data validation -> atomic charges calculation/biomacromolecular channel ^ conclusions.

O autorze

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/

Blurb

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.