A citation-based method for searching scientific literature

Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
Times Cited: 8333







List of co-cited articles
246 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
25

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
14

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
13

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

Automatic atom type and bond type perception in molecular mechanical calculations.
Junmei Wang, Wei Wang, Peter A Kollman, David A Case. J Mol Graph Model 2006
10

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
9

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
9

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

Lead- and drug-like compounds: the rule-of-five revolution.
Christopher A Lipinski. Drug Discov Today Technol 2004
7

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
7

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
Alexander W Schüttelkopf, Daan M F van Aalten. Acta Crystallogr D Biol Crystallogr 2004
7

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
7

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
7


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
7

Development and validation of a genetic algorithm for flexible docking.
G Jones, P Willett, R C Glen, A R Leach, R Taylor. J Mol Biol 1997
7

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
6

Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment.
Subramanian Boopathi, Adolfo B Poma, Ponmalai Kolandaivel. J Biomol Struct Dyn 2021
205
6


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
6

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
6


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
5


Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
Alexandra C Walls, Young-Jun Park, M Alejandra Tortorici, Abigail Wall, Andrew T McGuire, David Veesler. Cell 2020
5

A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2.
Rajib Islam, Md Rimon Parves, Archi Sundar Paul, Nizam Uddin, Md Sajjadur Rahman, Abdulla Al Mamun, Md Nayeem Hossain, Md Ackas Ali, Mohammad A Halim. J Biomol Struct Dyn 2021
124
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



PLIP: fully automated protein-ligand interaction profiler.
Sebastian Salentin, Sven Schreiber, V Joachim Haupt, Melissa F Adasme, Michael Schroeder. Nucleic Acids Res 2015
590
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 semiempirical free energy force field with charge-based desolvation.
Ruth Huey, Garrett M Morris, Arthur J Olson, David S Goodsell. J Comput Chem 2007
5

ZINC 15--Ligand Discovery for Everyone.
Teague Sterling, John J Irwin. J Chem Inf Model 2015
909
5

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
631
4

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R Miller, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, Adrian E Roitberg. J Chem Theory Comput 2012
4

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
4

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
4

VERIFY3D: assessment of protein models with three-dimensional profiles.
D Eisenberg, R Lüthy, J U Bowie. Methods Enzymol 1997
4

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
4


A new and rapid colorimetric determination of acetylcholinesterase activity.
G L ELLMAN, K D COURTNEY, V ANDRES, R M FEATHER-STONE. Biochem Pharmacol 1961
4

Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach.
Salman Ali Khan, Komal Zia, Sajda Ashraf, Reaz Uddin, Zaheer Ul-Haq. J Biomol Struct Dyn 2021
160
4

Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach.
Sukanth Kumar Enmozhi, Kavitha Raja, Irudhayasamy Sebastine, Jerrine Joseph. J Biomol Struct Dyn 2021
148
4


Peptide-like and small-molecule inhibitors against Covid-19.
Suyash Pant, Meenakshi Singh, V Ravichandiran, U S N Murty, Hemant Kumar Srivastava. J Biomol Struct Dyn 2021
153
4


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
4

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