A citation-based method for searching scientific literature

Ashkan Fakharzadeh, Jiahui Zhang, Christopher Roland, Celeste Sagui. Nucleic Acids Res 2022
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


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
244
60

Conformational changes of non-B DNA.
Jungkweon Choi, Tetsuro Majima. Chem Soc Rev 2011
210
40

Timeline: Z-DNA: the long road to biological function.
Alexander Rich, Shuguang Zhang. Nat Rev Genet 2003
329
40

Sequence-dependent cost for Z-form shapes the torsion-driven B-Z transition via close interplay of Z-DNA and DNA bubble.
Sook Ho Kim, Hae Jun Jung, Il-Buem Lee, Nam-Kyung Lee, Seok-Cheol Hong. Nucleic Acids Res 2021
8
40


Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.
Petra Kührová, Robert B Best, Sandro Bottaro, Giovanni Bussi, Jiří Šponer, Michal Otyepka, Pavel Banáš. J Chem Theory Comput 2016
73
40

High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.
Senada Nozinovic, Boris Fürtig, Hendrik R A Jonker, Christian Richter, Harald Schwalbe. Nucleic Acids Res 2010
126
40

Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications.
Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Thorben Fröhlking, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiří Šponer. J Chem Theory Comput 2022
4
50

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.
Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiří Šponer, Pavel Banáš. J Chem Theory Comput 2019
51
40

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.
Christina Bergonzo, Niel M Henriksen, Daniel R Roe, Thomas E Cheatham. RNA 2015
83
40


Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.
Asaminew H Aytenfisu, Aleksandar Spasic, Alan Grossfield, Harry A Stern, David H Mathews. J Chem Theory Comput 2017
63
40

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Jiří Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka,[...]. Chem Rev 2018
232
40

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
205
40

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
Jane S Richardson, Bohdan Schneider, Laura W Murray, Gary J Kapral, Robert M Immormino, Jeffrey J Headd, David C Richardson, Daniela Ham, Eli Hershkovits, Loren Dean Williams,[...]. RNA 2008
174
40

Mg2+ ions: do they bind to nucleobase nitrogens?
Filip Leonarski, Luigi D'Ascenzo, Pascal Auffinger. Nucleic Acids Res 2017
48
40

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.
Pavel Banáš, Daniel Hollas, Marie Zgarbová, Petr Jurečka, Modesto Orozco, Thomas E Cheatham, Jiří Šponer, Michal Otyepka. J Chem Theory Comput 2010
71
40


Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters.
Marie Zgarbová, F Javier Luque, Jiří Sponer, Thomas E Cheatham, Michal Otyepka, Petr Jurečka. J Chem Theory Comput 2013
192
40



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
569
40

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
459
40

The regulation and functions of DNA and RNA G-quadruplexes.
Dhaval Varshney, Jochen Spiegel, Katherine Zyner, David Tannahill, Shankar Balasubramanian. Nat Rev Mol Cell Biol 2020
308
40

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
40

Trinucleotide repeat disorders.
Harry T Orr, Huda Y Zoghbi. Annu Rev Neurosci 2007
40

Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy.
A R La Spada, E M Wilson, D B Lubahn, A E Harding, K H Fischbeck. Nature 1991
40

A nanothermometer based on the different pi stackings of B- and Z-DNA.
Ryu Tashiro, Hiroshi Sugiyama. Angew Chem Int Ed Engl 2003
49
20

Z-DNA's conformer substates revealed by FT-IR difference spectroscopy of nonoriented left-handed double helical poly(dG-dC).
Christine Rauch, Arthur Pichler, Michael Trieb, Bernd Wellenzohn, Klaus R Liedl, Erwin Mayer. J Biomol Struct Dyn 2005
11
20


Z-DNA and Z-RNA in human disease.
Alan Herbert. Commun Biol 2019
53
20

A nanomechanical device based on the B-Z transition of DNA.
C Mao, W Sun, Z Shen, N C Seeman. Nature 1999
464
20

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ alpha(ADAR1).
Sung Chul Ha, Jongkeun Choi, Hye-Yeon Hwang, Alexander Rich, Yang-Gyun Kim, Kyeong Kyu Kim. Nucleic Acids Res 2009
43
20


DNA damage and repair.
Errol C Friedberg. Nature 2003
581
20

Interactions of a tetraanionic porphyrin with DNA: from a Z-DNA sensor to a versatile supramolecular device.
Alessandro D'Urso, Angela Mammana, Milan Balaz, Andrea E Holmes, Nina Berova, Rosaria Lauceri, Roberto Purrello. J Am Chem Soc 2009
71
20


Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study.
Mahmoud Moradi, Volodymyr Babin, Christopher Roland, Celeste Sagui. Nucleic Acids Res 2013
30
20

Sequence-specific B-DNA flexibility modulates Z-DNA formation.
Jameson R Bothe, Ky Lowenhaupt, Hashim M Al-Hashimi. J Am Chem Soc 2011
26
20

A nanomotor involves a metastable, left-handed DNA duplex.
Yingmei Li, Chuan Zhang, Cheng Tian, Chengde Mao. Org Biomol Chem 2014
8
20



3D-NuS: A Web Server for Automated Modeling and Visualization of Non-Canonical 3-Dimensional Nucleic Acid Structures.
L Ponoop Prasad Patro, Abhishek Kumar, Narendar Kolimi, Thenmalarchelvi Rathinavelan. J Mol Biol 2017
25
20


Simultaneous morphological transformation of metal salt and conformations of DNA in a bio-based ionic liquid.
Jitkumar Bhatt, Matheus M Pereira, Kamalesh Prasad. Int J Biol Macromol 2019
2
50

Sequence-specific B-to-Z transition in self-assembled DNA: A biophysical and thermodynamic study.
Madhabi M Bhanjadeo, Bineeth Baral, Umakanta Subudhi. Int J Biol Macromol 2019
5
20

The effects of a neutral cosolute on the B to Z transition for DNA duplexes incorporating both CG and CA steps.
Pakinee Phromsiri, Rebecca R Gerling, Joshua M Blose. Nucleosides Nucleotides Nucleic Acids 2017
2
50


Lanthanum induced B-to-Z transition in self-assembled Y-shaped branched DNA structure.
Ashok K Nayak, Aseem Mishra, Bhabani S Jena, Barada K Mishra, Umakanta Subudhi. Sci Rep 2016
22
20

Twisting right to left: A…A mismatch in a CAG trinucleotide repeat overexpansion provokes left-handed Z-DNA conformation.
Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan. PLoS Comput Biol 2015
18
20


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.