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Copyright © 2015 BIF Centre, University of Kalyani.
Developed & Maintained by
BIF Centre,
Department of Biochemistry & Biophysics,
University of Kalyani, Kalyani,
Nadia-741 235,
West Bengal India.
In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound
to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or
binding affinity between two molecules.
The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a central role in
signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced. Therefore
docking is useful for predicting both the strength and type of signal produced.
Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn
predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs. Given the
biological and pharmaceutical significance of molecular docking, considerable efforts have been directed towards improving the methods
used to predict docking.
The following definitions are important for docking
Receptor: It is the receiving molecule or the host. The ligand binds to this molecule
Ligand: It is the molecule which binds to the receptor. This molecule brings about some changes in the Receptor.
Binding Mode: The relative orientation of the receptor with respect to the receptor is called the binding mode. It also reflects the
conformation of the ligand and receptor when bound together.
Docking may be of two different types, viz.,
The Rigid Body Docking and Flexible Docking.
Rigid Body Docking vs. Flexible Docking
If the bond angles, bond lengths and torsion angles of the components are not modified at any stage of docking procedure, it is known as
rigid body docking. A subject of speculation is whether or not rigid-body docking is sufficiently good for most docking. When substantial
conformational change occurs within the components at the time of docking, rigid-body docking is inadequate. However, scoring all possible
conformational changes is prohibitively expensive in computer time. Docking procedures which permit conformational change, or flexible
docking procedures, must intelligently select small subset of possible conformational changes for consideration.

REFERENCE:
1. Lengauer T, Rarey M (1996). "Computational methods for biomolecular docking". Curr. Opin. Struct. Biol. 6 (3): 402-6. doi:10.1016/S0959-
440X(96)80061-3. PMID 8804827
2. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004). "Docking and scoring in virtual screening for drug discovery: methods and applications".
Nature reviews. Drug discovery 3(11): 935-49. doi:10.1038/nrd1549. PMID 15520816
3. Jorgensen WL (1991). "Rusting of the lock and key model for protein-ligand binding".Science 254 (5034): 954-5.
doi:10.1126/science.1719636. PMID 1719636
4. Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK (2004). "Testing a flexible-receptor docking algorithm in a model binding site".
J. Mol. Biol. 337 (5): 1161-82.doi:10.1016/j.jmb.2004.02.015. PMID 15046985
5. Goldman BB, Wipke WT (2000). "QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock)".
Proteins 38 (1): 79-94.doi:10.1002/(SICI)1097-0134(20000101)38:1<79::AID-PROT9>3.0.CO;2-U.PMID 10651041
6. Meng EC, Shoichet BK, Kuntz ID (2004). "Automated docking with grid-based energy evaluation". Journal of Computational Chemistry 13
(4): 505-524.doi:10.1002/jcc.540130412
7. Kearsley SK, Underwood DJ, Sheridan RP, Miller MD (October 1994). "Flexibases: a way to enhance the use of molecular docking methods".
J. Comput. Aided Mol. Des. 8 (5): 565-82. doi:10.1007/BF00123666. PMID 7876901
8. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS
(March 2004). "Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy". J. Med. Chem.
47 (7): 1739-49. doi:10.1021/jm0306430. PMID 15027865
9. Cerqueira NM, Bras NF, Fernandes PA, Ramos MJ (January 2009). "MADAMM: a multistaged docking with an automated molecular
modeling protocol". Proteins 74 (1): 192-206. doi:10.1002/prot.22146. PMID 18618708
10. Totrov M, Abagyan R (April 2008). "Flexible ligand docking to multiple receptor conformations: a practical alternative". Curr. Opin. Struct.
Biol. 18 (2): 178-84.doi:10.1016/j.sbi.2008.01.004. PMC 2396190. PMID 18302984


Molecular docking
University of Kalyani, Nadia, West-Bengal, India.
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A DBT (Govt. of India) Sponsored Facility.
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