A citation-based method for searching scientific literature

Gregory A Babbitt, Miranda L Lynch, Matthew McCoy, Ernest P Fokoue, André O Hudson. J Biomol Struct Dyn 2022
Times Cited: 8







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



Times Cited
  Times     Co-cited
Similarity


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
62

DROIDS 3.0-Detecting Genetic and Drug Class Variant Impact on Conserved Protein Binding Dynamics.
Gregory A Babbitt, Ernest P Fokoue, Joshua R Evans, Kyle I Diller, Lily E Adams. Biophys J 2020
8
62

DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics.
Gregory A Babbitt, Jamie S Mortensen, Erin E Coppola, Lily E Adams, Justin K Liao. Biophys J 2018
10
62


The Amber biomolecular simulation programs.
David A Case, Thomas E Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J Woods. J Comput Chem 2005
62

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
50


Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.
Romelia Salomon-Ferrer, Andreas W Götz, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2013
50

Modeling of loops in protein structures.
A Fiser, R K Do, A Sali. Protein Sci 2000
50

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics.
Levi C T Pierce, Romelia Salomon-Ferrer, Cesar Augusto F de Oliveira, J Andrew McCammon, Ross C Walker. J Chem Theory Comput 2012
310
50

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.
Andreas W Götz, Mark J Williamson, Dong Xu, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2012
37

Functional binding dynamics relevant to the evolution of zoonotic spillovers in endemic and emergent Betacoronavirus strains.
Patrick Rynkiewicz, Miranda L Lynch, Feng Cui, André O Hudson, Gregory A Babbitt. J Biomol Struct Dyn 2021
4
75

Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2.
Khattab Al-Khafaji, Dunya Al-Duhaidahawi, Tugba Taskin Tok. J Biomol Struct Dyn 2021
77
25

A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury.
Keiji Kuba, Yumiko Imai, Shuan Rao, Hong Gao, Feng Guo, Bin Guan, Yi Huan, Peng Yang, Yanli Zhang, Wei Deng,[...]. Nat Med 2005
25

The flexibility of ACE2 in the context of SARS-CoV-2 infection.
Emilia P Barros, Lorenzo Casalino, Zied Gaieb, Abigail C Dommer, Yuzhang Wang, Lucy Fallon, Lauren Raguette, Kellon Belfon, Carlos Simmerling, Rommie E Amaro. Biophys J 2021
68
25



Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
Renhong Yan, Yuanyuan Zhang, Yaning Li, Lu Xia, Yingying Guo, Qiang Zhou. Science 2020
25

Structure of SARS coronavirus spike receptor-binding domain complexed with receptor.
Fang Li, Wenhui Li, Michael Farzan, Stephen C Harrison. Science 2005
25

Broad and Differential Animal Angiotensin-Converting Enzyme 2 Receptor Usage by SARS-CoV-2.
Xuesen Zhao, Danying Chen, Robert Szabla, Mei Zheng, Guoli Li, Pengcheng Du, Shuangli Zheng, Xinglin Li, Chuan Song, Rui Li,[...]. J Virol 2020
94
25


COVID-19 pandemic: Insights into structure, function, and hACE2 receptor recognition by SARS-CoV-2.
Anshumali Mittal, Kavyashree Manjunath, Rajesh Kumar Ranjan, Sandeep Kaushik, Sujeet Kumar, Vikash Verma. PLoS Pathog 2020
103
25



Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity.
Ludovico Cantuti-Castelvetri, Ravi Ojha, Liliana D Pedro, Minou Djannatian, Jonas Franz, Suvi Kuivanen, Franziska van der Meer, Katri Kallio, Tuğberk Kaya, Maria Anastasina,[...]. Science 2020
909
25

Detection of a SARS-CoV-2 variant of concern in South Africa.
Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi,[...]. Nature 2021
799
25

Structural basis for human coronavirus attachment to sialic acid receptors.
M Alejandra Tortorici, Alexandra C Walls, Yifei Lang, Chunyan Wang, Zeshi Li, Danielle Koerhuis, Geert-Jan Boons, Berend-Jan Bosch, Félix A Rey, Raoul J de Groot,[...]. Nat Struct Mol Biol 2019
328
25

The role of ACE2 in cardiovascular physiology.
Gavin Y Oudit, Michael A Crackower, Peter H Backx, Josef M Penninger. Trends Cardiovasc Med 2003
191
25

Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2.
Wenhui Li, Chengsheng Zhang, Jianhua Sui, Jens H Kuhn, Michael J Moore, Shiwen Luo, Swee-Kee Wong, I-Chueh Huang, Keming Xu, Natalya Vasilieva,[...]. EMBO J 2005
649
25

Neuropilin-1 is a host factor for SARS-CoV-2 infection.
James L Daly, Boris Simonetti, Katja Klein, Kai-En Chen, Maia Kavanagh Williamson, Carlos Antón-Plágaro, Deborah K Shoemark, Lorena Simón-Gracia, Michael Bauer, Reka Hollandi,[...]. Science 2020
643
25

Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
Yuan Yuan, Duanfang Cao, Yanfang Zhang, Jun Ma, Jianxun Qi, Qihui Wang, Guangwen Lu, Ying Wu, Jinghua Yan, Yi Shi,[...]. Nat Commun 2017
458
25

SARS-CoV-2 spike protein: flexibility as a new target for fighting infection.
Ciro Leonardo Pierri. Signal Transduct Target Ther 2020
22
25


Bat origins of MERS-CoV supported by bat coronavirus HKU4 usage of human receptor CD26.
Qihui Wang, Jianxun Qi, Yuan Yuan, Yifang Xuan, Pengcheng Han, Yuhua Wan, Wei Ji, Yan Li, Ying Wu, Jianwei Wang,[...]. Cell Host Microbe 2014
184
25


Human Coronavirus: Host-Pathogen Interaction.
To Sing Fung, Ding Xiang Liu. Annu Rev Microbiol 2019
504
25


Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV.
Xiuyuan Ou, Yan Liu, Xiaobo Lei, Pei Li, Dan Mi, Lili Ren, Li Guo, Ruixuan Guo, Ting Chen, Jiaxin Hu,[...]. Nat Commun 2020
25

Human coronavirus NL63 employs the severe acute respiratory syndrome coronavirus receptor for cellular entry.
Heike Hofmann, Krzysztof Pyrc, Lia van der Hoek, Martina Geier, Ben Berkhout, Stefan Pöhlmann. Proc Natl Acad Sci U S A 2005
471
25

Cell entry mechanisms of SARS-CoV-2.
Jian Shang, Yushun Wan, Chuming Luo, Gang Ye, Qibin Geng, Ashley Auerbach, Fang Li. Proc Natl Acad Sci U S A 2020
25

Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1.
Xiuyuan Ou, Hongxin Guan, Bo Qin, Zhixia Mu, Justyna A Wojdyla, Meitian Wang, Samuel R Dominguez, Zhaohui Qian, Sheng Cui. Nat Commun 2017
41
25


Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF.
Paul T C Wan, Mathew J Garnett, S Mark Roe, Sharlene Lee, Dan Niculescu-Duvaz, Valerie M Good, C Michael Jones, Christopher J Marshall, Caroline J Springer, David Barford,[...]. Cell 2004
25

RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E).
Poulikos I Poulikakos, Yogindra Persaud, Manickam Janakiraman, Xiangju Kong, Charles Ng, Gatien Moriceau, Hubing Shi, Mohammad Atefi, Bjoern Titz, May Tal Gabay,[...]. Nature 2011
25

Mutations of the BRAF gene in human cancer.
Helen Davies, Graham R Bignell, Charles Cox, Philip Stephens, Sarah Edkins, Sheila Clegg, Jon Teague, Hayley Woffendin, Mathew J Garnett, William Bottomley,[...]. Nature 2002
25

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
25

GLYCAM06: a generalizable biomolecular force field. Carbohydrates.
Karl N Kirschner, Austin B Yongye, Sarah M Tschampel, Jorge González-Outeiriño, Charlisa R Daniels, B Lachele Foley, Robert J Woods. J Comput Chem 2008
25

Vulnerabilities in coronavirus glycan shields despite extensive glycosylation.
Yasunori Watanabe, Zachary T Berndsen, Jayna Raghwani, Gemma E Seabright, Joel D Allen, Oliver G Pybus, Jason S McLellan, Ian A Wilson, Thomas A Bowden, Andrew B Ward,[...]. Nat Commun 2020
182
12

Site-specific glycan analysis of the SARS-CoV-2 spike.
Yasunori Watanabe, Joel D Allen, Daniel Wrapp, Jason S McLellan, Max Crispin. Science 2020
812
12

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Beata Turoňová, Mateusz Sikora, Christoph Schürmann, Wim J H Hagen, Sonja Welsch, Florian E C Blanc, Sören von Bülow, Michael Gecht, Katrin Bagola, Cindy Hörner,[...]. Science 2020
315
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.