Structural Bioinformatics Tools for Drug Design
Extraction of Biologically Relevant Information from Structural Databases
Page
%P
-
Article
Open AccessCorrection to: Optimized SQE atomic charges for peptides accessible via a web application
A Correction to this paper has been published: https://doi.org/10.1186/s13321-021-00528-w
-
Article
Open AccessOptimized SQE atomic charges for peptides accessible via a web application
Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity ...
-
Article
Open AccessUncovering of cytochrome P450 anatomy by SecStrAnnotator
Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can he...
-
Protocol
Visualization and Analysis of Protein Structures with LiteMol Suite
LiteMol suite is an innovative solution that enables near-instant delivery of model and experimental biomacromolecular structural data, providing users with an interactive and responsive experience in all mode...
-
Protocol
Automated Family-Wide Annotation of Secondary Structure Elements
Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the va...
-
Article
Behavior of BsoBI endonuclease in the presence and absence of DNA
BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA ...
-
Article
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data
-
Article
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...
-
Book
-
Chapter
Concluding Remarks
This chapter summarizes the purpose and goals of the book.
-
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 ...
-
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...
-
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...
-
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...
-
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...
-
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...
-
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 ...
-
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...
-
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...
-
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...
