Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
Times Cited: 1623
Times Cited: 1623
Times Cited
Times Co-cited
Similarity
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
Oleg Trott, Arthur J Olson. J Comput Chem 2010
Oleg Trott, Arthur J Olson. J Comput Chem 2010
28
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
26
GROMACS: fast, flexible, and free.
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
22
PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
Alexander W Schüttelkopf, Daan M F van Aalten. Acta Crystallogr D Biol Crystallogr 2004
Alexander W Schüttelkopf, Daan M F van Aalten. Acta Crystallogr D Biol Crystallogr 2004
19
UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
19
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.
Antoine Daina, Olivier Michielin, Vincent Zoete. Sci Rep 2017
Antoine Daina, Olivier Michielin, Vincent Zoete. Sci Rep 2017
17
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
15
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.
Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng,[...]. Nature 2020
Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng,[...]. Nature 2020
15
Electrostatics of nanosystems: application to microtubules and the ribosome.
N A Baker, D Sept, S Joseph, M J Holst, J A McCammon. Proc Natl Acad Sci U S A 2001
N A Baker, D Sept, S Joseph, M J Holst, J A McCammon. Proc Natl Acad Sci U S A 2001
15
pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures.
Douglas E V Pires, Tom L Blundell, David B Ascher. J Med Chem 2015
Douglas E V Pires, Tom L Blundell, David B Ascher. J Med Chem 2015
13
A Novel Coronavirus from Patients with Pneumonia in China, 2019.
Na Zhu, Dingyu Zhang, Wenling Wang, Xingwang Li, Bo Yang, Jingdong Song, Xiang Zhao, Baoying Huang, Weifeng Shi, Roujian Lu,[...]. N Engl J Med 2020
Na Zhu, Dingyu Zhang, Wenling Wang, Xingwang Li, Bo Yang, Jingdong Song, Xiang Zhao, Baoying Huang, Weifeng Shi, Roujian Lu,[...]. N Engl J Med 2020
12
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
P A Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, Y Duan, W Wang,[...]. Acc Chem Res 2000
P A Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, Y Duan, W Wang,[...]. Acc Chem Res 2000
12
Open Babel: An open chemical toolbox.
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison. J Cheminform 2011
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison. J Cheminform 2011
11
A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang,[...]. Nature 2020
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang,[...]. Nature 2020
11
LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
11
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
11
ACPYPE - AnteChamber PYthon Parser interfacE.
Alan W Sousa da Silva, Wim F Vranken. BMC Res Notes 2012
Alan W Sousa da Silva, Wim F Vranken. BMC Res Notes 2012
11
Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method.
Nadine Homeyer, Holger Gohlke. Mol Inform 2012
Nadine Homeyer, Holger Gohlke. Mol Inform 2012
9
The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
9
SwissParam: a fast force field generation tool for small organic molecules.
Vincent Zoete, Michel A Cuendet, Aurélien Grosdidier, Olivier Michielin. J Comput Chem 2011
Vincent Zoete, Michel A Cuendet, Aurélien Grosdidier, Olivier Michielin. J Comput Chem 2011
9
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings.
C A Lipinski, F Lombardo, B W Dominy, P J Feeney. Adv Drug Deliv Rev 2001
C A Lipinski, F Lombardo, B W Dominy, P J Feeney. Adv Drug Deliv Rev 2001
8
A new coronavirus associated with human respiratory disease in China.
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
8
SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
8
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel,[...]. Bioinformatics 2013
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel,[...]. Bioinformatics 2013
8
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
A C Wallace, R A Laskowski, J M Thornton. Protein Eng 1995
A C Wallace, R A Laskowski, J M Thornton. Protein Eng 1995
8
Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
8
Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
8
Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
7
Small-molecule library screening by docking with PyRx.
Sargis Dallakyan, Arthur J Olson. Methods Mol Biol 2015
Sargis Dallakyan, Arthur J Olson. Methods Mol Biol 2015
7
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation.
Berk Hess. J Chem Theory Comput 2008
Berk Hess. J Chem Theory Comput 2008
7
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.
Chris Oostenbrink, Alessandra Villa, Alan E Mark, Wilfred F van Gunsteren. J Comput Chem 2004
Chris Oostenbrink, Alessandra Villa, Alan E Mark, Wilfred F van Gunsteren. J Comput Chem 2004
7
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
7
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.
Roujian Lu, Xiang Zhao, Juan Li, Peihua Niu, Bo Yang, Honglong Wu, Wenling Wang, Hao Song, Baoying Huang, Na Zhu,[...]. Lancet 2020
Roujian Lu, Xiang Zhao, Juan Li, Peihua Niu, Bo Yang, Honglong Wu, Wenling Wang, Hao Song, Baoying Huang, Na Zhu,[...]. Lancet 2020
6
Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19.
Nisha Muralidharan, R Sakthivel, D Velmurugan, M Michael Gromiha. J Biomol Struct Dyn 2021
Nisha Muralidharan, R Sakthivel, D Velmurugan, M Michael Gromiha. J Biomol Struct Dyn 2021
6
Verification of protein structures: patterns of nonbonded atomic interactions.
C Colovos, T O Yeates. Protein Sci 1993
C Colovos, T O Yeates. Protein Sci 1993
6
Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro.
Manli Wang, Ruiyuan Cao, Leike Zhang, Xinglou Yang, Jia Liu, Mingyue Xu, Zhengli Shi, Zhihong Hu, Wu Zhong, Gengfu Xiao. Cell Res 2020
Manli Wang, Ruiyuan Cao, Leike Zhang, Xinglou Yang, Jia Liu, Mingyue Xu, Zhengli Shi, Zhihong Hu, Wu Zhong, Gengfu Xiao. Cell Res 2020
6
Therapeutic options for the 2019 novel coronavirus (2019-nCoV).
Guangdi Li, Erik De Clercq. Nat Rev Drug Discov 2020
Guangdi Li, Erik De Clercq. Nat Rev Drug Discov 2020
6
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
6
PubChem 2019 update: improved access to chemical data.
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu,[...]. Nucleic Acids Res 2019
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu,[...]. Nucleic Acids Res 2019
6
Lead- and drug-like compounds: the rule-of-five revolution.
Christopher A Lipinski. Drug Discov Today Technol 2004
Christopher A Lipinski. Drug Discov Today Technol 2004
6
DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
5
An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy.
Thanigaimalai Pillaiyar, Manoj Manickam, Vigneshwaran Namasivayam, Yoshio Hayashi, Sang-Hun Jung. J Med Chem 2016
Thanigaimalai Pillaiyar, Manoj Manickam, Vigneshwaran Namasivayam, Yoshio Hayashi, Sang-Hun Jung. J Med Chem 2016
5
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.
. Nat Microbiol 2020
. Nat Microbiol 2020
5
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
5
Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods.
Canrong Wu, Yang Liu, Yueying Yang, Peng Zhang, Wu Zhong, Yali Wang, Qiqi Wang, Yang Xu, Mingxue Li, Xingzhou Li,[...]. Acta Pharm Sin B 2020
Canrong Wu, Yang Liu, Yueying Yang, Peng Zhang, Wu Zhong, Yali Wang, Qiqi Wang, Yang Xu, Mingxue Li, Xingzhou Li,[...]. Acta Pharm Sin B 2020
5
The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds.
Yahira M Báez-Santos, Sarah E St John, Andrew D Mesecar. Antiviral Res 2015
Yahira M Báez-Santos, Sarah E St John, Andrew D Mesecar. Antiviral Res 2015
5
Definition and testing of the GROMOS force-field versions 54A7 and 54B7.
Nathan Schmid, Andreas P Eichenberger, Alexandra Choutko, Sereina Riniker, Moritz Winger, Alan E Mark, Wilfred F van Gunsteren. Eur Biophys J 2011
Nathan Schmid, Andreas P Eichenberger, Alexandra Choutko, Sereina Riniker, Moritz Winger, Alan E Mark, Wilfred F van Gunsteren. Eur Biophys J 2011
5
Secondary metabolites from spice and herbs as potential multitarget inhibitors of SARS-CoV-2 proteins.
Saurabh Gupta, Vishal Singh, Pritish Kumar Varadwaj, Navajeet Chakravartty, A V S Krishna Mohan Katta, Sivarama Prasad Lekkala, George Thomas, Srinivasan Narasimhan, Arjula R Reddy, V B Reddy Lachagari. J Biomol Struct Dyn 2022
Saurabh Gupta, Vishal Singh, Pritish Kumar Varadwaj, Navajeet Chakravartty, A V S Krishna Mohan Katta, Sivarama Prasad Lekkala, George Thomas, Srinivasan Narasimhan, Arjula R Reddy, V B Reddy Lachagari. J Biomol Struct Dyn 2022
8
Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2.
Yadi Zhou, Yuan Hou, Jiayu Shen, Yin Huang, William Martin, Feixiong Cheng. Cell Discov 2020
Yadi Zhou, Yuan Hou, Jiayu Shen, Yin Huang, William Martin, Feixiong Cheng. Cell Discov 2020
4
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.