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Molecular docking is a computer simulation methodology which predicts the binding affinity of the target protein with the ligand at the atomistic level. The most important goal of molecular docking studies is to predict the binding conformation of protein-ligand and to estimate its interaction. It is also one of the main tools for virtual screening procedures, where a library of several compounds is “docked” against one drug target returning the best hit. Identifying the active site of the target protein where the ligand will bind is the first important step which needs to be performed before docking. This can be performed using programs like Q-SiteFinder, LigA Site, Meta Pocket, and CASTp [32]. A molecular docking study where the process of docking is performed without predicting the active site is referred as “Blind Docking” [33]. Here, Tables 1.2 and 1.3 show some of the most common Molecular docking software programs along with their specifications.

 AutoDock: It is an automated program to predict ligand and protein (bio-macromolecular targets) interactions. With recent advancement in bimolecular, X-ray crystallography is helping to provide structural information of complex bio-molecules such as protein and nucleic acids. The structures can be taken/downloaded and can be used as targets for new drug molecules in controlling diseases and disorders of human, animal, and plant and understanding of fundamental aspects of biology [41]. It can be downloaded from http://www.scripps.edu/olson/forli/autodock_flex_rings.html (accessed 12.12.16).

 GOLD: Genetic Optimization for Ligand Docking is a genetic algorithm which provides docking of flexible ligand and a protein with flexible hydroxyl groups. The software uses a scoring function that is based on favorable conformations found in Cambridge Structural Database. The speed of GOLD and the reliability of its predictions depend on the control of different values of the genetic algorithm parameters. It provides reliable results both protein and ligand (http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx) (accessed 20.12.16).

Table 1.2 The list of molecular docking softwares is represented in tabular form.

S. no.	Name of software	Description	Reference
1	AutoDock	It performs automated docking of flexible ligands to macromolecules.	[34]
2	DockVision	It performs Monte Carlo, Genetic Algorithm, and database screening docking algorithms.	[35, 36]
3	GOLD	It helps in identifying correct binding modes of the active target molecules.	[37]
4	Docking Server	It provides a web-based interface for the molecular docking of protein and ligand.	[38]
5	SwissDock	It is a protein ligand server that is accessed through ExPASy.	[39]
6	CombiBUILD	It is a structure-based drug design program which helps in designing of combinatorial libraries.	[37]
7	QM Polarized Ligand Docking	It performs the function of both Glide and Q-Site applications of Schrodinger Suit.	[40]
8	Docking Server	It provides a web-based, easy to use interface for the molecular docking of protein and ligand.	[34]
10	Click2Drug	It is a protein ligand server that is accessed through ExPASy.	http://www.click2drug.org/

Table 1.3 The list of molecular docking tools is represented in tabular form.

Tool	Brief description with uses
BLAST	Basic local alignment search tool; used for sequencing of DNA and protein.
RasMol	Raster molecule tool; used for molecular visualization of RNA/DNA and protein.
Discovery studio	Software; used for modeling and simulation.
Pub Med	Free search engine; used for searching matter related to medical and life sciences.
PDB	Protein Data Bank; used to collect information related to macromolecule.
Chem Draw	They are a part of the Chem office program which are used for drawing chemical molecule.
Marvin Sketch	These are advanced chemical editors that are used for drawing chemical structures and reactions.
PubChem	Database; used to collect information about structure and physiochemical properties of chemical compound.
AutoDock	Software; used for molecular docking.