Validation and analyses of biomacromolecular ligand conformations

ŽUFANOVÁ, Zuzana, Radka SVOBODOVÁ VAŘEKOVÁ and Michaela WIMMEROVÁ. Validation and analyses of biomacromolecular ligand conformations. In CEITEC PhD Retreat II. 2017. ISBN 978-80-210-8550-3.

Basic information

• Original name: Validation and analyses of biomacromolecular ligand conformations
• Authors: ŽUFANOVÁ, Zuzana, Radka SVOBODOVÁ VAŘEKOVÁ and Michaela WIMMEROVÁ.
• Edition: CEITEC PhD Retreat II, 2017.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Science
• ISBN: 978-80-210-8550-3
• Keywords in English: structure validation; ligand conformation; MotiveValidator; ValidatorDB

Abstract

With the immense increase in biomolecular structural data stored in databases in recent years, validation methods have been developed to assess the quality and accuracy of the biomolecular structures. Currently, most the structure validation programs focus on the validation of biomacromolecules as opposed to small ligands. This progression has been primarily due to complications arising from the large chemical variability of ligands. Existing programs for ligand validation prioritize evaluation of the correctness of specific properties such as torsion angles, bond length, and atom clashes, or focus on annotation validation (validation by comparing the structure with a correct model). Examples of validation programs using annotation validation are MotiveValidator (MV) and ValidatorDB (VDB), both of which examine the ligand structure completeness, ligand chirality, and ligand annotation errors. In this work, we focus on extending the functionality of MV and VDB by developing methodology to validate the ligand conformation. Our methodology is based on obtaining correct models from the literature and other existing databases, and comparing the two structures using Ertl chemical scaffolds. Ertl scaffolds will allow us to perform more accurate analysis, as they feature information about key parts of ligands such as the central part of the molecule without acyclic parts, and exocyclic double bonds.