A citation-based method for searching scientific literature

Shiv Bharadwaj, Amit Dubey, Umesh Yadava, Sarad Kumar Mishra, Sang Gu Kang, Vivek Dhar Dwivedi. Brief Bioinform 2021
Times Cited: 16







List of co-cited articles
106 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
43

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
37


Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2.
Mohammad M Ghahremanpour, Julian Tirado-Rives, Maya Deshmukh, Joseph A Ippolito, Chun-Hui Zhang, Israel Cabeza de Vaca, Maria-Elena Liosi, Karen S Anderson, William L Jorgensen. ACS Med Chem Lett 2020
64
25

Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors.
Chunlong Ma, Yanmei Hu, Julia Alma Townsend, Panagiotis I Lagarias, Michael Thomas Marty, Antonios Kolocouris, Jun Wang. ACS Pharmacol Transl Sci 2020
54
25

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.
G Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman. J Comput Aided Mol Des 2013
18

Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein.
Firoz A Dain Md Opo, Mohammed M Rahman, Foysal Ahammad, Istiak Ahmed, Mohiuddin Ahmed Bhuiyan, Abdullah M Asiri. Sci Rep 2021
8
37

Small-molecule library screening by docking with PyRx.
Sargis Dallakyan, Arthur J Olson. Methods Mol Biol 2015
533
18

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z H Zhang, Tingjun Hou. Chem Rev 2019
271
18

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
18

α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment.
Linlin Zhang, Daizong Lin, Yuri Kusov, Yong Nian, Qingjun Ma, Jiang Wang, Albrecht von Brunn, Pieter Leyssen, Kristina Lanko, Johan Neyts,[...]. J Med Chem 2020
206
18

Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur.
Zhenming Jin, Yao Zhao, Yuan Sun, Bing Zhang, Haofeng Wang, Yan Wu, Yan Zhu, Chen Zhu, Tianyu Hu, Xiaoyu Du,[...]. Nat Struct Mol Biol 2020
155
18

Coronaviruses: an overview of their replication and pathogenesis.
Anthony R Fehr, Stanley Perlman. Methods Mol Biol 2015
18

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
18

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
830
18

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.
Donghyuk Shin, Rukmini Mukherjee, Diana Grewe, Denisa Bojkova, Kheewoong Baek, Anshu Bhattacharya, Laura Schulz, Marek Widera, Ahmad Reza Mehdipour, Georg Tascher,[...]. Nature 2020
259
18

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.
Wenhao Dai, Bing Zhang, Xia-Ming Jiang, Haixia Su, Jian Li, Yao Zhao, Xiong Xie, Zhenming Jin, Jingjing Peng, Fengjiang Liu,[...]. Science 2020
488
18

Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography.
Daniel W Kneller, Gwyndalyn Phillips, Hugh M O'Neill, Robert Jedrzejczak, Lucy Stols, Paul Langan, Andrzej Joachimiak, Leighton Coates, Andrey Kovalevsky. Nat Commun 2020
102
18

In Silico Drug Repurposing for SARS-CoV-2 Main Proteinase and Spike Proteins.
Irene Maffucci, Alessandro Contini. J Proteome Res 2020
16
18

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
18

Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro.
Hongbo Liu, Fei Ye, Qi Sun, Hao Liang, Chunmei Li, Siyang Li, Roujian Lu, Baoying Huang, Wenjie Tan, Luhua Lai. J Enzyme Inhib Med Chem 2021
36
18

Crystal structure of SARS-CoV-2 papain-like protease.
Xiaopan Gao, Bo Qin, Pu Chen, Kaixiang Zhu, Pengjiao Hou, Justyna Aleksandra Wojdyla, Meitian Wang, Sheng Cui. Acta Pharm Sin B 2021
68
18



Epigallocatechin-3-gallate, an active ingredient of Traditional Chinese Medicines, inhibits the 3CLpro activity of SARS-CoV-2.
Ashuai Du, Rong Zheng, Cyrollah Disoma, Shiqin Li, Zongpeng Chen, Sijia Li, Pinjia Liu, Yuzheng Zhou, Yilun Shen, Sixu Liu,[...]. Int J Biol Macromol 2021
21
18

Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.
Pedro Fong, Jonathan P McNamara, Ian H Hillier, Richard A Bryce. J Chem Inf Model 2009
38
12

Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity.
Kemel Arafet, Natalia Serrano-Aparicio, Alessio Lodola, Adrian J Mulholland, Florenci V González, Katarzyna Świderek, Vicent Moliner. Chem Sci 2020
25
12


Computational assessment of MCM2 transcriptional expression and identification of the prognostic biomarker for human breast cancer.
Abdus Samad, Farhana Haque, Zulkar Nain, Rahat Alam, Md Abdullah Al Noman, Mohammad Habibur Rahman Molla, Md Saddam Hossen, Md Raquibul Islam, Md Iqbal Khan, Foysal Ahammad. Heliyon 2020
8
25

Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach.
Abdus Samad, Foysal Ahammad, Zulkar Nain, Rahat Alam, Raihan Rahman Imon, Mahadi Hasan, Md Shahedur Rahman. J Biomol Struct Dyn 2022
33
12

Systems Pharmacology in Small Molecular Drug Discovery.
Wei Zhou, Yonghua Wang, Aiping Lu, Ge Zhang. Int J Mol Sci 2016
47
12

IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics.
Karthikeyan Mohanraj, Bagavathy Shanmugam Karthikeyan, R P Vivek-Ananth, R P Bharath Chand, S R Aparna, Pattulingam Mangalapandi, Areejit Samal. Sci Rep 2018
51
12

Contemporary Strategies and Current Trends in Designing Antiviral Drugs against Dengue Fever via Targeting Host-Based Approaches.
Foysal Ahammad, Tengku Rogayah Tengku Abd Rashid, Maizan Mohamed, Suriyea Tanbin, Fazia Adyani Ahmad Fuad. Microorganisms 2019
8
25

High expression of bone morphogenetic protein 1 (BMP1) is associated with a poor survival rate in human gastric cancer, a dataset approaches.
Jahirul Hasnat Rafi, Tamanna Jafar, Mohammad Turhan Pathan, Rumman Reza, Saiful Islam, Israt Jahan Sourna, Rahat Alam, Abdus Samad, Foysal Ahammad. Genomics 2021
6
33

Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2.
Shafi Mahmud, Mohammad Abu Raihan Uddin, Gobindo Kumar Paul, Mst Sharmin Sultana Shimu, Saiful Islam, Ekhtiar Rahman, Ariful Islam, Md Samiul Islam, Maria Meha Promi, Talha Bin Emran,[...]. Brief Bioinform 2021
18
12

A hierarchical approach to all-atom protein loop prediction.
Matthew P Jacobson, David L Pincus, Chaya S Rapp, Tyler J F Day, Barry Honig, David E Shaw, Richard A Friesner. Proteins 2004
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
12


New insights on the antiviral effects of chloroquine against coronavirus: what to expect for COVID-19?
Christian A Devaux, Jean-Marc Rolain, Philippe Colson, Didier Raoult. Int J Antimicrob Agents 2020
498
12


Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS.
Kuo-Chen Chou, Dong-Qing Wei, Wei-Zhu Zhong. Biochem Biophys Res Commun 2003
326
12

Current Prevention of COVID-19: Natural Products and Herbal Medicine.
Junqing Huang, Gabriel Tao, Jingwen Liu, Junming Cai, Zhongyu Huang, Jia-Xu Chen. Front Pharmacol 2020
34
12

RNA-dependent RNA polymerase (RdRp) inhibitors: The current landscape and repurposing for the COVID-19 pandemic.
Lei Tian, Taotao Qiang, Chengyuan Liang, Xiaodong Ren, Minyi Jia, Jiayun Zhang, Jingyi Li, Minge Wan, Xin YuWen, Han Li,[...]. Eur J Med Chem 2021
23
12

Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus.
Wenhui Li, Michael J Moore, Natalya Vasilieva, Jianhua Sui, Swee Kee Wong, Michael A Berne, Mohan Somasundaran, John L Sullivan, Katherine Luzuriaga, Thomas C Greenough,[...]. Nature 2003
12

Case of the Index Patient Who Caused Tertiary Transmission of COVID-19 Infection in Korea: the Application of Lopinavir/Ritonavir for the Treatment of COVID-19 Infected Pneumonia Monitored by Quantitative RT-PCR.
Jaegyun Lim, Seunghyun Jeon, Hyun Young Shin, Moon Jung Kim, Yu Min Seong, Wang Jun Lee, Kang Won Choe, Yu Min Kang, Baeckseung Lee, Sang Joon Park. J Korean Med Sci 2020
330
12

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
12

Structure of SARS coronavirus spike receptor-binding domain complexed with receptor.
Fang Li, Wenhui Li, Michael Farzan, Stephen C Harrison. Science 2005
12

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
12

Experimental Treatment with Favipiravir for COVID-19: An Open-Label Control Study.
Qingxian Cai, Minghui Yang, Dongjing Liu, Jun Chen, Dan Shu, Junxia Xia, Xuejiao Liao, Yuanbo Gu, Qiue Cai, Yang Yang,[...]. Engineering (Beijing) 2020
539
12

Teicoplanin: an alternative drug for the treatment of COVID-19?
Sophie Alexandra Baron, Christian Devaux, Philippe Colson, Didier Raoult, Jean-Marc Rolain. Int J Antimicrob Agents 2020
119
12


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.