A citation-based method for searching scientific literature

Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
Times Cited: 2748







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



Times Cited
  Times     Co-cited
Similarity


VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
41

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
32

CHARMM: the biomolecular simulation program.
B R Brooks, C L Brooks, A D Mackerell, L Nilsson, R J Petrella, B Roux, Y Won, G Archontis, C Bartels, S Boresch,[...]. J Comput Chem 2009
24

CHARMM36m: an improved force field for folded and intrinsically disordered proteins.
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
18

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
18

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
16

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
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
15

Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C Phillips, David J Hardy, Julio D C Maia, John E Stone, João V Ribeiro, Rafael C Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang,[...]. J Chem Phys 2020
454
15


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
12

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
11

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
11

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
9

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
K Vanommeslaeghe, E Hatcher, C Acharya, S Kundu, S Zhong, J Shim, E Darian, O Guvench, P Lopes, I Vorobyov,[...]. J Comput Chem 2010
8

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
874
8


All-atom empirical potential for molecular modeling and dynamics studies of proteins.
A D MacKerell, D Bashford, M Bellott, R L Dunbrack, J D Evanseck, M J Field, S Fischer, J Gao, H Guo, S Ha,[...]. J Phys Chem B 1998
8

The MARTINI force field: coarse grained model for biomolecular simulations.
Siewert J Marrink, H Jelger Risselada, Serge Yefimov, D Peter Tieleman, Alex H de Vries. J Phys Chem B 2007
8

PACKMOL: a package for building initial configurations for molecular dynamics simulations.
L Martínez, R Andrade, E G Birgin, J M Martínez. J Comput Chem 2009
8

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
7

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
7



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
888
6


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
6


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
160
6

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.
Robert B Best, Xiao Zhu, Jihyun Shim, Pedro E M Lopes, Jeetain Mittal, Michael Feig, Alexander D Mackerell. J Chem Theory Comput 2012
6

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
6

Lipid14: The Amber Lipid Force Field.
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
694
5

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field.
Yifei Qi, Helgi I Ingólfsson, Xi Cheng, Jumin Lee, Siewert J Marrink, Wonpil Im. J Chem Theory Comput 2015
172
5

CHARMM-GUI supports the Amber force fields.
Jumin Lee, Manuel Hitzenberger, Manuel Rieger, Nathan R Kern, Martin Zacharias, Wonpil Im. J Chem Phys 2020
41
12

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations.
Tsjerk A Wassenaar, Helgi I Ingólfsson, Rainer A Böckmann, D Peter Tieleman, Siewert J Marrink. J Chem Theory Comput 2015
463
5

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
5

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Paul D Adams, Pavel V Afonine, Gábor Bunkóczi, Vincent B Chen, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Li-Wei Hung, Gary J Kapral, Ralf W Grosse-Kunstleve,[...]. Acta Crystallogr D Biol Crystallogr 2010
5

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
5

The MARTINI Coarse-Grained Force Field: Extension to Proteins.
Luca Monticelli, Senthil K Kandasamy, Xavier Periole, Ronald G Larson, D Peter Tieleman, Siewert-Jan Marrink. J Chem Theory Comput 2008
5

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein.
Lorenzo Casalino, Zied Gaieb, Jory A Goldsmith, Christy K Hjorth, Abigail C Dommer, Aoife M Harbison, Carl A Fogarty, Emilia P Barros, Bryn C Taylor, Jason S McLellan,[...]. ACS Cent Sci 2020
343
5

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern,[...]. PLoS Comput Biol 2017
609
5

Membrane lipids: where they are and how they behave.
Gerrit van Meer, Dennis R Voelker, Gerald W Feigenson. Nat Rev Mol Cell Biol 2008
5

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
5


Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
5

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
4

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.
Todd J Dolinsky, Jens E Nielsen, J Andrew McCammon, Nathan A Baker. Nucleic Acids Res 2004
4


Electrostatics of nanosystems: application to microtubules and the ribosome.
N A Baker, D Sept, S Joseph, M J Holst, J A McCammon. Proc Natl Acad Sci U S A 2001
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.