An Overview of Molecular Docking

Amol S. Dighe; Ansari Eram Tajamulhaq.

doi:10.52711/2231-5691.2024.00053

Asian Journal of Pharmaceutical Research

ISSN

2231-5691 (Online)
2231-5683 (Print)

Submit Article

An Overview of Molecular Docking

Author(s): Amol S. Dighe, Ansari Eram Tajamulhaq.

Email(s): amoldighe143@gmail.com

DOI: 10.52711/2231-5691.2024.00053

Address: Amol S. Dighe, Ansari Eram Tajamulhaq.
Pravara Rural College of Pharmacy, Loni.
*Corresponding Author

Published In: Volume - 14, Issue - 3, Year - 2024

View HTML

Purchase PDF

ABSTRACT:
The computational modeling of structural complexes formed by two or more interacting molecules is known as molecular docking. Prediction of an interesting three-dimensional structure is the primary goal of molecular docking. Software for molecular docking is mostly employed in the development of drugs. Molecules and the simple use of structural databases caused damage to an important mechanism. Several expensive tools for drug design and research are provided by molecular docking. Simple molecular prediction as well as rapid access to structural databases have become important components on the medicinal chemist's desktop. Virtual screening is the most important contribution of molecular docking. Numerous docking programs were used to visualize the three-dimensional structure of the molecule, and different computational techniques can be used to analyze docking gain. In structural molecular biology and computer-aided drug design, molecular docking is a key tool. Docking is useful for lead optimization because it can be used to do virtual screening on huge collections of compounds, rate the results, and provide structural ideas for how the ligands affect the target.

Keywords:

Cite this article:
Amol S. Dighe, Ansari Eram Tajamulhaq.. An Overview of Molecular Docking. Asian Journal of Pharmaceutical Research. 2024; 14(3):336-0. doi: 10.52711/2231-5691.2024.00053

Cite(Electronic):
Amol S. Dighe, Ansari Eram Tajamulhaq.. An Overview of Molecular Docking. Asian Journal of Pharmaceutical Research. 2024; 14(3):336-0. doi: 10.52711/2231-5691.2024.00053 Available on: https://asianjpr.com/AbstractView.aspx?PID=2024-14-3-22

REFERENCES:
1.    Jorgensen WL. The many roles of computation in drug discovery. Science. 2004; 303 (5665): 1813–1818.
2.    Bhagat, Rani and Butle, Santosh and Khobragade, Deepak and Wankhede, Sagar and Prasad, Chandani and Mahure, Divyani and Armarkar, Ashwini. Molecular Docking in Drug Discovery. Journal of Pharmaceutical Research International. 2021; 46-58.
3.    Dnyandev, Khemnar and Galave, Vishal and Kulkarni, Vaishali and Chandrakant, Menkudale and Otari, Kishor. A Review on Molecular Docking. International Research Journal of Pure and Applied Chemistry. 2021; 60-68.
4.    Lengauer T, Rarey M. et al. Computational methods for biomolecular docking. Current Opinion in Structural Biology. 1986; 6(3): 402–406.
5.    Kitchen DB, Decornez H, Furr JR, Bajorath J. et al. Docking and scoring in virtual screening for drug discovery: Methods and Applications. 2004; 3(11)
6.    Bajorath J. Integration of virtual and high-throughput screening. Nat Rev Drug Discov. 2002; 1(11): 882–894.
7.    Koshland DE Jr. Correlation of structure and function in enzyme action. Science.1963; 142:1533–1541.
8.    Hammes GG. Multiple conformational changes in enzyme catalysis. Biochemistry. 2002; 41(26): 8221–8228.
9.    Rarey M, Kramer B, Lengauer T, Klebe G.A fast flexible docking method using an incremental construction algorithm. J Mol Biol. 1996; 261(3): 470–489.
10.    Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins. 2002; 47(4):409–443.
11.    Coupez B, Lewis RA. Docking and scoring--theoretically easy, practically impossible? Curr Med Chem. 2006; 13(25): 2995–3003.
12.    Kontoyianni M, Madhav P, Suchanek E, Seibel W. Theoretical and practical considerations in virtual screening: A beaten field? Curr Med Chem. 2008; 15(2):107–116. [PubMed] [Google Scholar]
13.    Brooijmans N, Kuntz ID. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct. 2003; 32:335–373.
14.    Ten Brink T, Exner TE. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. J Chem Inf Model. 2009; 49(6):1535–1546.
15.    Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model. 2009; 49(6):1455–1474.
16.    Li X, Li Y, Cheng T, Liu Z, Wang R. Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes. J Comput Chem. 2010; 31(11): 2109–2125.
17.    Perola E, Walters WP, Charifson PS. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins. 2004; 56(2): 235–249.
18.    Huang N, Shoichet BK, Irwin JJ, et al. Benchmarking sets for molecular docking. Journal of Medicinal Chemistry. 2006; 49(23): 6789–801.
19.    Ballante F, Marshall GR, et al. An automated strategy for binding-pose selection and docking assessment in structure-based drug design. Journal of Chemical Information and Modeling. 2016; 56.
20.    Bursulaya BD, Totrov M, Abagyan R, Brooks CL, et al. Comparative study of several algorithms for flexible ligand docking. Journal of Computer Aided Molecular Design. 2003; 17(11): 755–63.
21.    Ballante Flavio, et al. Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection. Methods in Molecular Biology. 2018; 1824:67–88.
22.    Irwin JJ, et al. Community benchmarks for virtual screening. Journal of ComputerAided Molecular Design. 2018; 22(3–4):193–9.
23.    Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WT, Mortenson PN, Murray CW. et al. Diverse, high-quality test set for the validation of protein-ligand docking performance. Journal of Medicinal Chemistry. 2007: 50(4): 726–41.
24.    Hauser AS, Windshügel B, et al. A benchmark data set for assessment of peptide docking performance. Journal of Chemical Information and Modeling. 2015; 56(1):188–200.
25.    Mitchell JBO, Laskowski RA, Alex A, Thornton JM. Bleep-potential of mean force describing protein-ligand interactions: I. generating potential. J. Comput. Chem. 1999; 20(11): 1165–1176.
26.    Clark RD, Strizhev A, Leonard JM, Blake JF, Matthew JB. Consensus scoring for ligand/protein interactions. J Mol Graph Model. 2002; 20(4):281–295.
27.    Jorgensen WL. The many roles of computation in drug discovery. Science. 2004; 303(5665):1813–1818.

Recomonded Articles:

A Review on Natural Binders used in Pharmacy

Author(s): Subhashis Debnath, C. Navya Yadav, N. Nowjiya, M. Prabhavathi, A. SaiKumar, P. Sai Krishna, M. Niranjan Babu

DOI: 10.5958/2231-5691.2019.00009.1 Access: Open Access Read More

Significance of Pharmaceutical Excipients on Solid Dosage form Development: A Brief Review

Author(s): Sandesh Narayan Somnache, Ajeet Madhukar Godbole, Pankaj Sadashiv Gajare, Sapna Kashyap

DOI: 10.5958/2231-5691.2016.00028.9 Access: Open Access Read More

Formulation and Evaluation of Cinitapride Controlled Release Tablets

Author(s): Mercy Mathew, Ravikumar, Simila Madathil, Anju Govind, Narayana Swamy VB

DOI: 10.5958/2231-5691.2016.00015.0 Access: Open Access Read More

Formulation and Evaluation of Controlled Release Matrix Tablets of Labetalol HCl

Author(s): Niyaz Kavugoli, Ravikumar, Narayanaswamy VB

DOI: 10.5958/2231-5691.2016.00018.6 Access: Open Access Read More

Development and Validation of Memantine Hydrochloride by RP-HPLC Method

Author(s): Ayesha Anees, Asra Ali Bahazeq, MD. Muzaffar-Ur-Rehman, Syed Akbar, Juveria Mehveen

DOI: 10.5958/2231-5691.2019.00011.X Access: Open Access Read More

A Review on-Novel Approaches in Nanorobotics

Author(s): Lalita Balasaheb Patil, Swapnil S. Patil, Manoj M. Nitalikar, Chandrakant S. Magdum, Shrinivas K. Mohite

DOI: 10.5958/2231-5691.2016.00030.7 Access: Open Access Read More

A Review of the Pharmacological properties of potential drugs for the treatment of stuttering from the past to the future

Author(s): Tomasz W. Kamiński, Małgorzata Karbowska, Dariusz Pawlak

DOI: 10.5958/2231-5691.2018.00018.7 Access: Open Access Read More

Cultivation, Composting, Biochemical and Molecular Characterization of Calocybe indica (C and A)

Author(s): V. Saranya, P.Madhanraj, A. Panneerselvam

DOI: Access: Open Access Read More

Development and Evaluation of Telmisartan Pulsatile Drug Delivery by using Response Surface Methodology

Author(s): Indrajeet S. Patil, Omkar A. Patil, Girish Chandra R. Mandake, Manoj M. Nitalikar

DOI: 10.5958/2231-5691.2018.00035.7 Access: Open Access Read More

Review on Anti-inflammatory Properties of Mangrove plants

Author(s): P. Lalitha, V. Sachithanandam, N. S. Swarnakumar, R. Sridhar

DOI: 10.5958/2231-5691.2019.00045.5 Access: Open Access Read More

Synthesis, In silico Molecular Docking Study and Anti-bacterial Evaluation of some Novel 4-Anilino Quinazolines

Author(s): K. Hemalatha, Joseph Selvin, K. Girija

DOI: 10.5958/2231-5691.2018.00022.9 Access: Open Access Read More

Formulation Development and In-Vitro Evaluation of Extended Release Tablets Containing Losartan Potassium

Author(s): B. Babu Rao, P. Harish, Saikat Das, T. Ashwin Kumar, V. Raman Koundinya

DOI: Access: Open Access Read More

Liposomes: A Novel Drug Delivery System: An Overview

Author(s): Nikita R. Nikam, Priyanka R. Patil, R. R. Vakhariya, C. S. Magdum

DOI: 10.5958/2231-5691.2020.00005.2 Access: Open Access Read More

Evaluation of Prokaryotic and Eukaryotic Cell

Author(s): Ravi Kumar

DOI: 10.52711/2231-5691.2021.00036 Access: Open Access Read More

Comparative Study of Gatifloxacin and Sparfloxacin as Quinolone Antibiotics: An Overview

Author(s): Mr. Bhushan P. Gayakwad, . Shashikant D. Barhate, Prafull P. Patil, . Mayur S. Jain

DOI: 10.5958/2231-5691.2018.00009.6 Access: Open Access Read More

A Review on Natural Treatment’s of Vitiligo

Author(s): Ravi Kumar, Sachin Tyagi

DOI: 10.5958/2231-5691.2020.00046.5 Access: Open Access Read More

Biosensors: Current tool for Medication and Diagnosis

Author(s): Punasiya Rakesh, Patel Pramod, Pillai Sujit

DOI: 10.5958/2231-5691.2019.00006.6 Access: Open Access Read More

Osteoporosis: The Brittle Bone

Author(s): Bhagyashri T. Sakat, R B. Sakhare, U C. Suryvanshi, P. S. Kore, . S. K. Mohite, . C. S. Magdum

DOI: 10.5958/2231-5691.2018.00008.4 Access: Open Access Read More

Computational Studies and Synthesis of few Thiazolidine-2,4-Dion Analogues for Peroxisome Proliferator Activator Receptor- γ Agonist as Useful Antidiabetic Agent

Author(s): Shital N. Chaskar, Sanjay J. Kshirsagar

DOI: 10.5958/2231-5691.2017.00042.9 Access: Open Access Read More

Preparation of meloxicam spherical agglomerates to improve dissolution rate

Author(s): S. Sujani, R. Hari Babu , K. Ravindra Reddy

DOI: Access: Open Access Read More

Asian Journal of Pharmaceutical Research (AJPRes.) is an international, peer-reviewed journal, devoted to pharmaceutical sciences. AJPRes. publishes Original Research Articles, Short Communications..... Read more >>>

RNI: Not Available
DOI: 10.5958/2231–5691