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Journal of Biomolecular Structure and Dynamics Volume 29, 2011 - Issue 1
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Original Articles

BetaDock: Shape-Priority Docking Method Based on Beta-Complex

Deok-Soo Kim Department of Industrial Engineering, Hanyang University, Seoul, South Korea
,
Chong-Min Kim Voronoi Diagram Research Center, Hanyang University, Seoul, South Korea
,
Chung-In Won Department of Industrial Engineering, Hanyang University, Seoul, South Korea
,
Jae-Kwan Kim Department of Industrial Engineering, Hanyang University, Seoul, South Korea
,
Joonghyun Ryu Voronoi Diagram Research Center, Hanyang University, Seoul, South Korea
,
Youngsong Cho Voronoi Diagram Research Center, Hanyang University, Seoul, South Korea
,
Changhee Lee Mechatronics and Manufacturing Technology Center, Samsung Electronics, Suwon, South Korea
&
Jong Bhak Theragen, Suwon, South Korea
 show all
Pages 219-242 | Received 05 Jan 2011, Published online: 15 May 2012

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Rajender Kumar, Prabha Garg & P.V. Bharatam. (2015) Shape-based virtual screening, docking, and molecular dynamics simulations to identify Mtb-ASADH inhibitors. Journal of Biomolecular Structure and Dynamics 33:5, pages 1082-1093.
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Jae-Kwan Kim & Deok-Soo Kim. (2012) BetaSuperposer: superposition of protein surfaces using beta-shapes. Journal of Biomolecular Structure and Dynamics 30:6, pages 684-700.
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Articles from other publishers (28)

Asif Alavi & Vikas Sharma. (2023) Role of Docking in Anticancer Drug Discovery. Letters in Drug Design & Discovery 20:10, pages 1490-1511.
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Changsoo Lee, Jinsol Yang, Sohee Kwon & Chaok Seok. (2023) GalaxyDock2‐HEME : P rotein–ligand docking for heme proteins . Journal of Computational Chemistry 44:14, pages 1369-1380.
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Arushi Sharma & Ragothaman M. Yennamalli. 2023. Basic Biotechniques for Bioprocess and Bioentrepreneurship. Basic Biotechniques for Bioprocess and Bioentrepreneurship 243 258 .
Ömür Baysal & Ragıp Soner Silme. 2021. SARS-CoV-2 Origin and COVID-19 Pandemic Across the Globe. SARS-CoV-2 Origin and COVID-19 Pandemic Across the Globe.
Anantha Krishnan Dhanabalan, Mamangam Subaraja, Kuppusamy Palanichamy, Devadasan Velmurugan & Krishnasamy Gunasekaran. (2021) Identification of a Chlorogenic Ester as a Monoamine Oxidase (MAO-B) Inhibitor by Integrating “Traditional and Machine Learning” Virtual Screening and In Vitro as well as In Vivo Validation: A Lead against Neurodegenerative Disorders?. ACS Chemical Neuroscience 12:19, pages 3690-3707.
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Donald J. AbrahamFrancesca Spyrakis, Aurijit Sarkar & Glen E. Kellogg. 2003. Burger's Medicinal Chemistry and Drug Discovery. Burger's Medicinal Chemistry and Drug Discovery 1 102 .
Vishnu Kumar SharmaPrasad V. Bharatam. (2021) Identification of Selective Inhibitors of Ld DHFR Enzyme Using Pharmacoinformatic Methods . Journal of Computational Biology 28:1, pages 43-59.
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Vinay Kumar, N. Sushma Sri, Neha Tripathi, Vishnu K. Sharma, Prasad V. Bharatam, Prabha Garg & Sushma Singh. (2020) Structural exploration of glutamine synthetase from Leishmania donovani: Insights from in silico and in vitro analysis. International Journal of Biological Macromolecules 146, pages 860-874.
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Xiang Li, Adarsh Krishnamurthy, Iddo Hanniel & Sara McMains. (2019) Edge topology construction of Voronoi diagrams of spheres in non-general position. Computers & Graphics 82, pages 332-342.
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Shafi Ullah Khan, Nafees Ahemad, Lay-Hong Chuah, Rakesh Naidu & Thet Thet Htar. (2019) Sequential ligand- and structure-based virtual screening approach for the identification of potential G protein-coupled estrogen receptor-1 (GPER-1) modulators. RSC Advances 9:5, pages 2525-2538.
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Nikhil Bachappanavar & Sinosh Skariyachan. 2019. Essentials of Bioinformatics, Volume II. Essentials of Bioinformatics, Volume II 233 281 .
Hari K. Voruganti & Bhaskar Dasgupta. (2018) A novel volumetric criterion for optimal shape matching of surfaces for protein-protein docking. Journal of Computational Design and Engineering 5:2, pages 180-190.
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Marzieh Karimian Amroabadi, Asghar Taheri-Kafrani, Leily Heidarpoor Saremi & Ali Asghar Rastegari. (2018) Spectroscopic studies of the interaction between alprazolam and apo-human serum transferrin as a drug carrier protein. International Journal of Biological Macromolecules 108, pages 263-271.
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Azizeh Abdolmaleki, Fereshteh Shiri & Jahan B. Ghasemi. 2019. Multi-Target Drug Design Using Chem-Bioinformatic Approaches. Multi-Target Drug Design Using Chem-Bioinformatic Approaches 51 90 .
Sinosh Skariyachan. 2017. Translational Bioinformatics and Its Application. Translational Bioinformatics and Its Application 89 117 .
Enrico Glaab. (2016) Building a virtual ligand screening pipeline using free software: a survey. Briefings in Bioinformatics 17:2, pages 352-366.
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Woong-Hee Shin, Xiaolei Zhu, Mark Bures & Daisuke Kihara. (2015) Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery. Molecules 20:7, pages 12841-12862.
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Jae-Kwan Kim, Chung-In Won, Jehyun Cha, Kichun Lee & Deok-Soo Kim. (2015) Optimal Ligand Descriptor for Pocket Recognition Based on the Beta-Shape. PLOS ONE 10:4, pages e0122787.
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Yu-Chian Chen. (2015) Beware of docking!. Trends in Pharmacological Sciences 36:2, pages 78-95.
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Jae-Kwan Kim, Youngsong Cho, Roman A Laskowski, Seong Eon Ryu, Kokichi Sugihara & Deok-Soo Kim. (2014) BetaVoid: Molecular voids via beta-complexes and Voronoi diagrams. Proteins: Structure, Function, and Bioinformatics 82:9, pages 1829-1849.
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Jae Kwan Kim, Youngsong Cho, Mokwon Lee, Jehyun Cha, Chanyoung Song, Deok Soo Kim & Donguk Kim. (2014) BetaConcept: A Program for Voronoi Diagrams, Dual Structures, and Complexes in the Plane. BetaConcept: A Program for Voronoi Diagrams, Dual Structures, and Complexes in the Plane.
C. George Priya Doss, Chiranjib Chakraborty, Vaishnavi Narayan & D. Thirumal Kumar. 2014. 365 423 .
Woong-Hee Shin, Jae-Kwan Kim, Deok-Soo Kim & Chaok Seok. (2013) GalaxyDock2: Protein-ligand docking using beta-complex and global optimization. Journal of Computational Chemistry 34:30, pages 2647-2656.
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Elizabeth Yuriev & Paul A. Ramsland. (2013) Latest developments in molecular docking: 2010-2011 in review. Journal of Molecular Recognition 26:5, pages 215-239.
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Deok-Soo Kim, Youngsong Cho, Joonghyun Ryu, Jae-Kwan Kim & Donguk Kim. (2013) Anomalies in quasi-triangulations and beta-complexes of spherical atoms in molecules. Computer-Aided Design 45:1, pages 35-52.
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Deok-Soo Kim, Youngsong Cho, Jae-Kwan Kim & Kokichi Sugihara. 2013. Transactions on Computational Science XX. Transactions on Computational Science XX 92 111 .
Deok-Soo Kim. 2013. Handbook of Combinatorial Optimization. Handbook of Combinatorial Optimization 2685 2740 .
Deok-Soo Kim & Kokichi Sugihara. (2012) Tunnels and Voids in Molecules via Voronoi Diagram. Tunnels and Voids in Molecules via Voronoi Diagram.

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