A citation-based method for searching scientific literature

Pietro Delre, Fabiana Caporuscio, Michele Saviano, Giuseppe Felice Mangiatordi. Front Chem 2020
Times Cited: 25







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



Times Cited
  Times     Co-cited
Similarity


Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Jerzy Osipiuk, Saara-Anne Azizi, Steve Dvorkin, Michael Endres, Robert Jedrzejczak, Krysten A Jones, Soowon Kang, Rahul S Kathayat, Youngchang Kim, Vladislav G Lisnyak,[...]. Nat Commun 2021
135
64

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
426
56

Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.
Wioletta Rut, Zongyang Lv, Mikolaj Zmudzinski, Stephanie Patchett, Digant Nayak, Scott J Snipas, Farid El Oualid, Tony T Huang, Miklos Bekes, Marcin Drag,[...]. Sci Adv 2020
191
48

Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.
Theresa Klemm, Gregor Ebert, Dale J Calleja, Cody C Allison, Lachlan W Richardson, Jonathan P Bernardini, Bernadine Gc Lu, Nathan W Kuchel, Christoph Grohmann, Yuri Shibata,[...]. EMBO J 2020
178
44

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
36

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
32

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
456
32

Repurposing of FDA-approved antivirals, antibiotics, anthelmintics, antioxidants, and cell protectives against SARS-CoV-2 papain-like protease.
Mahmoud Kandeel, Alaa H M Abdelrahman, Kentaro Oh-Hashi, Abdelazim Ibrahim, Katharigatta N Venugopala, Mohamed A Morsy, Mahmoud A A Ibrahim. J Biomol Struct Dyn 2021
47
32

The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery.
Ziyang Fu, Bin Huang, Jinle Tang, Shuyan Liu, Ming Liu, Yuxin Ye, Zhihong Liu, Yuxian Xiong, Wenning Zhu, Dan Cao,[...]. Nat Commun 2021
85
32


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
121
28

Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease.
Brendan T Freitas, Ian A Durie, Jackelyn Murray, Jaron E Longo, Holden C Miller, David Crich, Robert Jeff Hogan, Ralph A Tripp, Scott D Pegan. ACS Infect Dis 2020
140
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
24

A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication.
Kiira Ratia, Scott Pegan, Jun Takayama, Katrina Sleeman, Melissa Coughlin, Surendranath Baliji, Rima Chaudhuri, Wentao Fu, Bellur S Prabhakar, Michael E Johnson,[...]. Proc Natl Acad Sci U S A 2008
281
24

Supporting SARS-CoV-2 Papain-Like Protease Drug Discovery: In silico Methods and Benchmarking.
Tamer M Ibrahim, Muhammad I Ismail, Matthias R Bauer, Adnan A Bekhit, Frank M Boeckler. Front Chem 2020
17
35

Molecular docking of potential SARS-CoV-2 papain-like protease inhibitors.
Daoqun Li, Junwen Luan, Leiliang Zhang. Biochem Biophys Res Commun 2021
16
37

Structure-Based Screening to Discover New Inhibitors for Papain-like Proteinase of SARS-CoV-2: An In Silico Study.
Mostafa Jamalan, Ebrahim Barzegari, Fathollah Gholami-Borujeni. J Proteome Res 2021
12
50

Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay.
Chunlong Ma, Michael Dominic Sacco, Zilei Xia, George Lambrinidis, Julia Alma Townsend, Yanmei Hu, Xiangzhi Meng, Tommy Szeto, Mandy Ba, Xiujun Zhang,[...]. ACS Cent Sci 2021
39
24

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
20

Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs.
Valentina L Kouznetsova, Aidan Zhang, Mahidhar Tatineni, Mark A Miller, Igor F Tsigelny. PeerJ 2020
29
20

SARS-CoV-2: the many pros of targeting PLpro.
Christopher B McClain, Nicolas Vabret. Signal Transduct Target Ther 2020
23
21

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
20

High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors.
Yao Zhao, Xiaoyu Du, Yinkai Duan, Xiaoyan Pan, Yifang Sun, Tian You, Lin Han, Zhenming Jin, Weijuan Shang, Jing Yu,[...]. Protein Cell 2021
38
20

Dual targeting of 3CLpro and PLpro of SARS-CoV-2: A novel structure-based design approach to treat COVID-19.
Sajjan Rajpoot, Manikandan Alagumuthu, Mirza S Baig. Curr Res Struct Biol 2021
28
20

Repurposing clinically approved drugs for COVID-19 treatment targeting SARS-CoV-2 papain-like protease.
Yunxia Xu, Ke Chen, Juanli Pan, Yingshou Lei, Danting Zhang, Lipei Fang, Jinle Tang, Xin Chen, Yanhong Ma, Yi Zheng,[...]. Int J Biol Macromol 2021
15
33

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
16

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2.
Olujide O Olubiyi, Maryam Olagunju, Monika Keutmann, Jennifer Loschwitz, Birgit Strodel. Molecules 2020
56
16


Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study.
Davide Gentile, Vincenzo Patamia, Angela Scala, Maria Teresa Sciortino, Anna Piperno, Antonio Rescifina. Mar Drugs 2020
157
16

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
16

Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease.
Kiira Ratia, Andrew Kilianski, Yahira M Baez-Santos, Susan C Baker, Andrew Mesecar. PLoS Pathog 2014
132
16

Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches.
Mubarak A Alamri, Muhammad Tahir Ul Qamar, Muhammad Usman Mirza, Safar M Alqahtani, Matheus Froeyen, Ling-Ling Chen. J Pharm Anal 2020
35
16


The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
16

Can Papain-like Protease Inhibitors Halt SARS-CoV-2 Replication?
Biplab K Maiti. ACS Pharmacol Transl Sci 2020
21
19


Insights Into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 Papain-Like Protease.
Yuliana K Bosken, Timothy Cholko, Yuan-Chao Lou, Kuen-Phon Wu, Chia-En A Chang. Front Mol Biosci 2020
25
16

Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs.
Maryam Hosseini, Wanqiu Chen, Daliao Xiao, Charles Wang. Precis Clin Med 2021
34
16

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2.
Ewelina Weglarz-Tomczak, Jakub M Tomczak, Michał Talma, Małgorzata Burda-Grabowska, Mirosław Giurg, Stanley Brul. Sci Rep 2021
36
16

Multi-targeting of functional cysteines in multiple conserved SARS-CoV-2 domains by clinically safe Zn-ejectors.
Karen Sargsyan, Chien-Chu Lin, Ting Chen, Cédric Grauffel, Yi-Ping Chen, Wei-Zen Yang, Hanna S Yuan, Carmay Lim. Chem Sci 2020
40
16

Remdesivir for the Treatment of Covid-19 - Final Report.
John H Beigel, Kay M Tomashek, Lori E Dodd, Aneesh K Mehta, Barry S Zingman, Andre C Kalil, Elizabeth Hohmann, Helen Y Chu, Annie Luetkemeyer, Susan Kline,[...]. N Engl J Med 2020
12

Scalable molecular dynamics with NAMD.
James C Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D Skeel, Laxmikant Kalé, Klaus Schulten. J Comput Chem 2005
12


Ensemble Docking in Drug Discovery.
Rommie E Amaro, Jerome Baudry, John Chodera, Özlem Demir, J Andrew McCammon, Yinglong Miao, Jeremy C Smith. Biophys J 2018
180
12

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
12



Ligand and structure-based virtual screening applied to the SARS-CoV-2 main protease: an in silico repurposing study.
Witor Ribeiro Ferraz, Renan Augusto Gomes, Andre Luis S Novaes, Gustavo Henrique Goulart Trossini. Future Med Chem 2020
47
12

A comprehensive review on promising anti-viral therapeutic candidates identified against main protease from SARS-CoV-2 through various computational methods.
Ekampreet Singh, Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Rashmi Prabha Singh, Jayaraman Muthukumaran, Amit Kumar Singh. J Genet Eng Biotechnol 2020
19
15

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