A citation-based method for searching scientific literature

Alexander W Schüttelkopf, Daan M F van Aalten. Acta Crystallogr D Biol Crystallogr 2004
Times Cited: 3417







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



Times Cited
  Times     Co-cited
Similarity


g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
35

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
31

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
30


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
17

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
13

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
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


VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
12

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
11

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
10

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
10

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
10



The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
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
8

PLIP: fully automated protein-ligand interaction profiler.
Sebastian Salentin, Sven Schreiber, V Joachim Haupt, Melissa F Adasme, Michael Schroeder. Nucleic Acids Res 2015
657
8

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
8

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
A C Wallace, R A Laskowski, J M Thornton. Protein Eng 1995
7

DataWarrior: an open-source program for chemistry aware data visualization and analysis.
Thomas Sander, Joel Freyss, Modest von Korff, Christian Rufener. J Chem Inf Model 2015
458
7

admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties.
Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Shen, Zengrui Wu, Guixia Liu, Philip W Lee, Yun Tang. J Chem Inf Model 2012
682
7

PubChem Substance and Compound databases.
Sunghwan Kim, Paul A Thiessen, Evan E Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A Shoemaker,[...]. Nucleic Acids Res 2016
7


ZINC: a free tool to discover chemistry for biology.
John J Irwin, Teague Sterling, Michael M Mysinger, Erin S Bolstad, Ryan G Coleman. J Chem Inf Model 2012
6

Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs.
Kanchan Anand, John Ziebuhr, Parvesh Wadhwani, Jeroen R Mesters, Rolf Hilgenfeld. Science 2003
975
6


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
6

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study.
Nanshan Chen, Min Zhou, Xuan Dong, Jieming Qu, Fengyun Gong, Yang Han, Yang Qiu, Jingli Wang, Ying Liu, Yuan Wei,[...]. Lancet 2020
6

Overview of the CCP4 suite and current developments.
Martyn D Winn, Charles C Ballard, Kevin D Cowtan, Eleanor J Dodson, Paul Emsley, Phil R Evans, Ronan M Keegan, Eugene B Krissinel, Andrew G W Leslie, Airlie McCoy,[...]. Acta Crystallogr D Biol Crystallogr 2011
6

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
5

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
5

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
5

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
5

Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors.
Vijay Kumar Bhardwaj, Rahul Singh, Jatin Sharma, Vidya Rajendran, Rituraj Purohit, Sanjay Kumar. J Biomol Struct Dyn 2021
143
5

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
5

Essential dynamics of proteins.
A Amadei, A B Linssen, H J Berendsen. Proteins 1993
5

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.
Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R Hutchison. J Cheminform 2012
5

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
5

Lead- and drug-like compounds: the rule-of-five revolution.
Christopher A Lipinski. Drug Discov Today Technol 2004
5

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
Richard A Friesner, Jay L Banks, Robert B Murphy, Thomas A Halgren, Jasna J Klicic, Daniel T Mainz, Matthew P Repasky, Eric H Knoll, Mee Shelley, Jason K Perry,[...]. J Med Chem 2004
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
5

Molecular properties that influence the oral bioavailability of drug candidates.
Daniel F Veber, Stephen R Johnson, Hung-Yuan Cheng, Brian R Smith, Keith W Ward, Kenneth D Kopple. J Med Chem 2002
5





Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
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.