A citation-based method for searching scientific literature

Qifeng Bai, Shuoyan Tan, Tingyang Xu, Huanxiang Liu, Junzhou Huang, Xiaojun Yao. Brief Bioinform 2021
Times Cited: 23







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



Times Cited
  Times     Co-cited
Similarity


Deep reinforcement learning for de novo drug design.
Mariya Popova, Olexandr Isayev, Alexander Tropsha. Sci Adv 2018
227
34

COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19.
Ren Kong, Guangbo Yang, Rui Xue, Ming Liu, Feng Wang, Jianping Hu, Xiaoqiang Guo, Shan Chang. Bioinformatics 2020
61
26

Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research.
Zhiwei Feng, Maozi Chen, Tianjian Liang, Mingzhe Shen, Hui Chen, Xiang-Qun Xie. Brief Bioinform 2021
13
46

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules.
Rafael Gómez-Bombarelli, Jennifer N Wei, David Duvenaud, José Miguel Hernández-Lobato, Benjamín Sánchez-Lengeling, Dennis Sheberla, Jorge Aguilera-Iparraguirre, Timothy D Hirzel, Ryan P Adams, Alán Aspuru-Guzik. ACS Cent Sci 2018
507
26

The rise of deep learning in drug discovery.
Hongming Chen, Ola Engkvist, Yinhai Wang, Marcus Olivecrona, Thomas Blaschke. Drug Discov Today 2018
373
26

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
21

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
21

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
677
21


SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
21

Deep learning enables rapid identification of potent DDR1 kinase inhibitors.
Alex Zhavoronkov, Yan A Ivanenkov, Alex Aliper, Mark S Veselov, Vladimir A Aladinskiy, Anastasiya V Aladinskaya, Victor A Terentiev, Daniil A Polykovskiy, Maksim D Kuznetsov, Arip Asadulaev,[...]. Nat Biotechnol 2019
200
21

GuacaMol: Benchmarking Models for de Novo Molecular Design.
Nathan Brown, Marco Fiscato, Marwin H S Segler, Alain C Vaucher. J Chem Inf Model 2019
109
21


Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks.
Marwin H S Segler, Thierry Kogej, Christian Tyrchan, Mark P Waller. ACS Cent Sci 2018
316
21

ZINC 15--Ligand Discovery for Everyone.
Teague Sterling, John J Irwin. J Chem Inf Model 2015
909
21

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
21

ChEMBL: towards direct deposition of bioassay data.
David Mendez, Anna Gaulton, A Patrícia Bento, Jon Chambers, Marleen De Veij, Eloy Félix, María Paula Magariños, Juan F Mosquera, Prudence Mutowo, Michal Nowotka,[...]. Nucleic Acids Res 2019
293
21

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
17

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
17

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
17

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
17

D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19.
Yulong Shi, Xinben Zhang, Kaijie Mu, Cheng Peng, Zhengdan Zhu, Xiaoyu Wang, Yanqing Yang, Zhijian Xu, Weiliang Zhu. Acta Pharm Sin B 2020
34
17

Long short-term memory.
S Hochreiter, J Schmidhuber. Neural Comput 1997
17

Molecular generative model based on conditional variational autoencoder for de novo molecular design.
Jaechang Lim, Seongok Ryu, Jin Woo Kim, Woo Youn Kim. J Cheminform 2018
59
17

Generative Recurrent Networks for De Novo Drug Design.
Anvita Gupta, Alex T Müller, Berend J H Huisman, Jens A Fuchs, Petra Schneider, Gisbert Schneider. Mol Inform 2018
121
17

Adversarial Threshold Neural Computer for Molecular de Novo Design.
Evgeny Putin, Arip Asadulaev, Quentin Vanhaelen, Yan Ivanenkov, Anastasia V Aladinskaya, Alex Aliper, Alex Zhavoronkov. Mol Pharm 2018
56
17

Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds.
Anh-Tien Ton, Francesco Gentile, Michael Hsing, Fuqiang Ban, Artem Cherkasov. Mol Inform 2020
195
17

Molecular de-novo design through deep reinforcement learning.
Marcus Olivecrona, Thomas Blaschke, Ola Engkvist, Hongming Chen. J Cheminform 2017
218
17

Shape-Based Generative Modeling for de Novo Drug Design.
Miha Skalic, José Jiménez, Davide Sabbadin, Gianni De Fabritiis. J Chem Inf Model 2019
47
17

De Novo Design of Bioactive Small Molecules by Artificial Intelligence.
Daniel Merk, Lukas Friedrich, Francesca Grisoni, Gisbert Schneider. Mol Inform 2018
103
17


Application of Generative Autoencoder in De Novo Molecular Design.
Thomas Blaschke, Marcus Olivecrona, Ola Engkvist, Jürgen Bajorath, Hongming Chen. Mol Inform 2018
119
17

Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17.
Lars Ruddigkeit, Ruud van Deursen, Lorenz C Blum, Jean-Louis Reymond. J Chem Inf Model 2012
342
17

Rethinking drug design in the artificial intelligence era.
Petra Schneider, W Patrick Walters, Alleyn T Plowright, Norman Sieroka, Jennifer Listgarten, Robert A Goodnow, Jasmin Fisher, Johanna M Jansen, José S Duca, Thomas S Rush,[...]. Nat Rev Drug Discov 2020
104
17

From Target to Drug: Generative Modeling for the Multimodal Structure-Based Ligand Design.
Miha Skalic, Davide Sabbadin, Boris Sattarov, Simone Sciabola, Gianni De Fabritiis. Mol Pharm 2019
18
22

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.
Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta,[...]. Nucleic Acids Res 2019
422
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
13

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
13

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
13

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
David E Gordon, Gwendolyn M Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M White, Matthew J O'Meara, Veronica V Rezelj, Jeffrey Z Guo, Danielle L Swaney,[...]. Nature 2020
13

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
13

Drug repurposing: progress, challenges and recommendations.
Sudeep Pushpakom, Francesco Iorio, Patrick A Eyers, K Jane Escott, Shirley Hopper, Andrew Wells, Andrew Doig, Tim Guilliams, Joanna Latimer, Christine McNamee,[...]. Nat Rev Drug Discov 2019
956
13

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
916
13

CORDITE: The Curated CORona Drug InTERactions Database for SARS-CoV-2.
Roman Martin, Hannah F Löchel, Marius Welzel, Georges Hattab, Anne-Christin Hauschild, Dominik Heider. iScience 2020
13
23

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
13

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
13

A de novo molecular generation method using latent vector based generative adversarial network.
Oleksii Prykhodko, Simon Viet Johansson, Panagiotis-Christos Kotsias, Josep Arús-Pous, Esben Jannik Bjerrum, Ola Engkvist, Hongming Chen. J Cheminform 2019
40
13


Bidirectional Molecule Generation with Recurrent Neural Networks.
Francesca Grisoni, Michael Moret, Robin Lingwood, Gisbert Schneider. J Chem Inf Model 2020
21
14

DeepScaffold: A Comprehensive Tool for Scaffold-Based De Novo Drug Discovery Using Deep Learning.
Yibo Li, Jianxing Hu, Yanxing Wang, Jielong Zhou, Liangren Zhang, Zhenming Liu. J Chem Inf Model 2020
21
14


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.