A citation-based method for searching scientific literature

Katarina Hart, Nicolas Foloppe, Christopher M Baker, Elizabeth J Denning, Lennart Nilsson, Alexander D Mackerell. J Chem Theory Comput 2012
Times Cited: 312







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



Times Cited
  Times     Co-cited
Similarity


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
46

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
37

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
26

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.
Elizabeth J Denning, U Deva Priyakumar, Lennart Nilsson, Alexander D Mackerell. J Comput Chem 2011
232
22

CHARMM-GUI: a web-based graphical user interface for CHARMM.
Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
20

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
19

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
18

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

Parmbsc1: a refined force field for DNA simulations.
Ivan Ivani, Pablo D Dans, Agnes Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu,[...]. Nat Methods 2016
422
18

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.
Alberto Pérez, Iván Marchán, Daniel Svozil, Jiri Sponer, Thomas E Cheatham, Charles A Laughton, Modesto Orozco. Biophys J 2007
18

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
17

Assessing the Current State of Amber Force Field Modifications for DNA.
Rodrigo Galindo-Murillo, James C Robertson, Marie Zgarbová, Jiří Šponer, Michal Otyepka, Petr Jurečka, Thomas E Cheatham. J Chem Theory Comput 2016
189
14

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
13

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
13

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
11

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.
Marie Zgarbová, Jiří Šponer, Michal Otyepka, Thomas E Cheatham, Rodrigo Galindo-Murillo, Petr Jurečka. J Chem Theory Comput 2015
229
11

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.
Marie Zgarbová, Michal Otyepka, Jiří Sponer, Arnošt Mládek, Pavel Banáš, Thomas E Cheatham, Petr Jurečka. J Chem Theory Comput 2011
541
10

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
9

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
9

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
9

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
9

A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.
Janamejaya Chowdhary, Edward Harder, Pedro E M Lopes, Lei Huang, Alexander D MacKerell, Benoît Roux. J Phys Chem B 2013
109
8




High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
Wei Jiang, David J Hardy, James C Phillips, Alexander D Mackerell, Klaus Schulten, Benoît Roux. J Phys Chem Lett 2011
164
8

Quadruplex DNA: sequence, topology and structure.
Sarah Burge, Gary N Parkinson, Pascale Hazel, Alan K Todd, Stephen Neidle. Nucleic Acids Res 2006
8

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations.
Konstantinos Gkionis, Holger Kruse, James A Platts, Arnošt Mládek, Jaroslav Koča, Jiří Šponer. J Chem Theory Comput 2014
59
13



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
8

Crystal structure of the nucleosome core particle at 2.8 A resolution.
K Luger, A W Mäder, R K Richmond, D F Sargent, T J Richmond. Nature 1997
8

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.
Haibo Yu, Troy W Whitfield, Edward Harder, Guillaume Lamoureux, Igor Vorobyov, Victor M Anisimov, Alexander D Mackerell, Benoît Roux. J Chem Theory Comput 2010
273
7


Structure of a B-DNA dodecamer: conformation and dynamics.
H R Drew, R M Wing, T Takano, C Broka, S Tanaka, K Itakura, R E Dickerson. Proc Natl Acad Sci U S A 1981
880
7



RNA force field with accuracy comparable to state-of-the-art protein force fields.
Dazhi Tan, Stefano Piana, Robert M Dirks, David E Shaw. Proc Natl Acad Sci U S A 2018
106
7

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.
Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, Jay W Ponder, Pengyu Ren. J Chem Theory Comput 2018
100
7


Polarizable force field for RNA based on the classical drude oscillator.
Justin A Lemkul, Alexander D MacKerell. J Comput Chem 2018
40
15

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.
Olgun Guvench, Sairam S Mallajosyula, E Prabhu Raman, Elizabeth Hatcher, Kenno Vanommeslaeghe, Theresa J Foster, Francis W Jamison, Alexander D Mackerell. J Chem Theory Comput 2011
336
6

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
6


How accurate are accurate force-fields for B-DNA?
Pablo D Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco. Nucleic Acids Res 2017
67
8

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes.
Marek Havrila, Petr Stadlbauer, Barira Islam, Michal Otyepka, Jiří Šponer. J Chem Theory Comput 2017
35
17


Improved Force Field Parameters Lead to a Better Description of RNA Structure.
Christina Bergonzo, Thomas E Cheatham. J Chem Theory Comput 2015
75
8




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.