A citation-based method for searching scientific literature

Callum J Dickson, Benjamin D Madej, Age A Skjevik, Robin M Betz, Knut Teigen, Ian R Gould, Ross C Walker. J Chem Theory Comput 2014
Times Cited: 651







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



Times Cited
  Times     Co-cited
Similarity


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
51

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
35

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
30


CHARMM-GUI: a web-based graphical user interface for CHARMM.
Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
24

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.
Emilia L Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C Song, Eder M Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M Venable,[...]. J Comput Chem 2014
930
16

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
16


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
14

New ways to boost molecular dynamics simulations.
Elmar Krieger, Gert Vriend. J Comput Chem 2015
314
13

OPM database and PPM web server: resources for positioning of proteins in membranes.
Mikhail A Lomize, Irina D Pogozheva, Hyeon Joo, Henry I Mosberg, Andrei L Lomize. Nucleic Acids Res 2012
833
12

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.
Sunhwan Jo, Joseph B Lim, Jeffery B Klauda, Wonpil Im. Biophys J 2009
826
12

Fast empirical pKa prediction by Ewald summation.
Elmar Krieger, Jens E Nielsen, Chris A E M Spronk, Gert Vriend. J Mol Graph Model 2006
199
11

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
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

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
9


Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.
Jeffery B Klauda, Richard M Venable, J Alfredo Freites, Joseph W O'Connor, Douglas J Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D MacKerell, Richard W Pastor. J Phys Chem B 2010
8



H++: a server for estimating pKas and adding missing hydrogens to macromolecules.
John C Gordon, Jonathan B Myers, Timothy Folta, Valia Shoja, Lenwood S Heath, Alexey Onufriev. Nucleic Acids Res 2005
836
7


LIPID11: a modular framework for lipid simulations using amber.
Åge A Skjevik, Benjamin D Madej, Ross C Walker, Knut Teigen. J Phys Chem B 2012
132
7

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
133
6

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
6

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.
Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, Oliver Beckstein. J Comput Chem 2011
960
6

Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
6

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
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

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


The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
5

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z H Zhang, Tingjun Hou. Chem Rev 2019
339
5

MCPB.py: A Python Based Metal Center Parameter Builder.
Pengfei Li, Kenneth M Merz. J Chem Inf Model 2016
186
5

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Jumin Lee, Xi Cheng, Jason M Swails, Min Sun Yeom, Peter K Eastman, Justin A Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi,[...]. J Chem Theory Comput 2016
5

Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization.
Elmar Krieger, Roland L Dunbrack, Rob W W Hooft, Barbara Krieger. Methods Mol Biol 2012
97
5

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
954
5







CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.
Jumin Lee, Dhilon S Patel, Jonas Ståhle, Sang-Jun Park, Nathan R Kern, Seonghoon Kim, Joonseong Lee, Xi Cheng, Miguel A Valvano, Otto Holst,[...]. J Chem Theory Comput 2019
139
5

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

Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation.
Md Jahirul Islam, Akib Mahmud Khan, Md Rimon Parves, Md Nayeem Hossain, Mohammad A Halim. Sci Rep 2019
22
18

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
4

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
4

Making optimal use of empirical energy functions: force-field parameterization in crystal space.
Elmar Krieger, Tom Darden, Sander B Nabuurs, Alexei Finkelstein, Gert Vriend. Proteins 2004
569
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.