The Comparison of Docking Search Algorithms and Scoring Functions: An Overview and Case Studies

The Comparison of Docking Search Algorithms and Scoring Functions: An Overview and Case Studies

Marjana Novič (National Institute of Chemistry, Slovenia), Tjaša Tibaut (National Institute of Chemistry, Slovenia), Marko Anderluh (University of Ljubljana, Slovenia), Jure Borišek (National Institute of Chemistry, Slovenia) and Tihomir Tomašič (University of Ljubljana, Slovenia)
Copyright: © 2017 |Pages: 30
DOI: 10.4018/978-1-5225-1762-7.ch032
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Abstract

This chapter, composed of two parts, firstly provides molecular docking overview and secondly two molecular docking case studies are described. In overview, basic information about molecular docking are presented such as description of search algorithms and scoring functions applied in various docking programs. Brief description of methods utilized in some of the most popular docking programs also applied in our experimental work is provided. AutoDock, CDOCKER, GOLD, FlexX and FRED were used for docking studies of the DC-SIGN protein, while GOLD was further used for docking studies of cathepsin K protein. Methods and results of our studies with their contribution to science and medicine are presented. Content of the chapter is therefore appropriate for public of Medicinal and Organic Chemistry as an overview of docking studies, and also for Computational Chemists at the beginning of their work as the introduction to application of molecular docking programs.
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Background

Molecular docking, in the case of small molecules also known as ligand docking, can be defined as computational method for prediction of the structure of ligand-receptor complexes. Ligand docking process involves two basic steps: prediction of ligand conformation and orientation (the pose) by search algorithms and assessment of binding affinity by scoring functions.

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