A citation-based method for searching scientific literature


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



Times Cited
  Times     Co-cited
Similarity




History of the ribosome and the origin of translation.
Anton S Petrov, Burak Gulen, Ashlyn M Norris, Nicholas A Kovacs, Chad R Bernier, Kathryn A Lanier, George E Fox, Stephen C Harvey, Roger M Wartell, Nicholas V Hud,[...]. Proc Natl Acad Sci U S A 2015
109
100

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.
Ilyas Yildirim, Harry A Stern, Scott D Kennedy, Jason D Tubbs, Douglas H Turner. J Chem Theory Comput 2010
106
100

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
215
100

Molecular view of ligands specificity for CAG repeats in anti-Huntington therapy.
Anna Bochicchio, Giulia Rossetti, Oriana Tabarrini, Sybille Krauβ, Paolo Carloni. J Chem Theory Comput 2015
10
100

Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.
Louis G Smith, Zhen Tan, Aleksandar Spasic, Debapratim Dutta, Leslie A Salas-Estrada, Alan Grossfield, David H Mathews. J Chem Theory Comput 2018
5
100

Targeting RNA with small molecules.
Jason R Thomas, Paul J Hergenrother. Chem Rev 2008
419
100

Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein.
Amy Davidson, Thomas C Leeper, Zafiria Athanassiou, Krystyna Patora-Komisarska, Jonathan Karn, John A Robinson, Gabriele Varani. Proc Natl Acad Sci U S A 2009
112
100

The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.
Weiwei He, Yen-Lin Chen, Lois Pollack, Serdal Kirmizialtin. Sci Adv 2021
2
100

Principles for targeting RNA with drug-like small molecules.
Katherine Deigan Warner, Christine E Hajdin, Kevin M Weeks. Nat Rev Drug Discov 2018
180
100



Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B.
C Faber, H Sticht, K Schweimer, P Rösch. J Biol Chem 2000
114
100


MID1, mutated in Opitz syndrome, encodes an ubiquitin ligase that targets phosphatase 2A for degradation.
A Trockenbacher, V Suckow, J Foerster, J Winter, S Krauss, H H Ropers, R Schneider, S Schweiger. Nat Genet 2001
222
100

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
365
100

CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration.
Shaohong Peng, Pei Guo, Xiao Lin, Ying An, Kong Hung Sze, Matthew Ho Yan Lau, Zhefan Stephen Chen, Qianwen Wang, Wen Li, Jacquelyne Ka-Li Sun,[...]. Proc Natl Acad Sci U S A 2021
2
100

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.
Jiří Šponer, Pavel Banáš, Petr Jurečka, Marie Zgarbová, Petra Kührová, Marek Havrila, Miroslav Krepl, Petr Stadlbauer, Michal Otyepka. J Phys Chem Lett 2014
95
100

How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape.
Michael F Bardaro, Zahra Shajani, Krystyna Patora-Komisarska, John A Robinson, Gabriele Varani. Nucleic Acids Res 2009
53
100

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
37
100


Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases.
Agnieszka Kiliszek, Ryszard Kierzek, Wlodzimierz J Krzyzosiak, Wojciech Rypniewski. Nucleic Acids Res 2010
59
100


Protein structure-based drug design: from docking to molecular dynamics.
Paweł Śledź, Amedeo Caflisch. Curr Opin Struct Biol 2018
152
100

Discovery of Potential Inhibitors for RNA-Dependent RNA Polymerase of Norovirus: Virtual Screening, and Molecular Dynamics.
Oluwakemi Ebenezer, Maryam A Jordaan, Nkululeko Damoyi, Michael Shapi. Int J Mol Sci 2020
1
100

Ribonuclease dicer cleaves triplet repeat hairpins into shorter repeats that silence specific targets.
Jacek Krol, Agnieszka Fiszer, Agnieszka Mykowska, Krzysztof Sobczak, Mateusz de Mezer, Wlodzimierz J Krzyzosiak. Mol Cell 2007
131
100

Role of conformational heterogeneity in ligand recognition by viral RNA molecules.
Lev Levintov, Harish Vashisth. Phys Chem Chem Phys 2021
1
100

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
79
100




Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts.
Amit Kumar, Raman Parkesh, Lukasz J Sznajder, Jessica L Childs-Disney, Krzysztof Sobczak, Matthew D Disney. ACS Chem Biol 2012
59
100

Water dispersion interactions strongly influence simulated structural properties of disordered protein states.
Stefano Piana, Alexander G Donchev, Paul Robustelli, David E Shaw. J Phys Chem B 2015
377
100


Protein-RNA interactions: a structural analysis.
S Jones, D T Daley, N M Luscombe, H M Berman, J M Thornton. Nucleic Acids Res 2001
289
100

Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides.
Vojtěch Mlýnský, Petra Kührová, Tomáš Kühr, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiří Šponer. J Chem Theory Comput 2020
9
100

Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein.
Amy Davidson, Krystyna Patora-Komisarska, John A Robinson, Gabriele Varani. Nucleic Acids Res 2011
50
100

The P42 peptide and Peptide-based therapies for Huntington's disease.
Cecilia Marelli, Florence Maschat. Orphanet J Rare Dis 2016
12
100

Exploring RNA structure and dynamics through enhanced sampling simulations.
Vojtěch Mlýnský, Giovanni Bussi. Curr Opin Struct Biol 2018
13
100

Control of mTORC1 signaling by the Opitz syndrome protein MID1.
Enbo Liu, Christine A Knutzen, Sybille Krauss, Susann Schweiger, Gary G Chiang. Proc Natl Acad Sci U S A 2011
57
100

Toward empirical force fields that match experimental observables.
Thorben Fröhlking, Mattia Bernetti, Nicola Calonaci, Giovanni Bussi. J Chem Phys 2020
9
100

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations.
Trang N Do, Paolo Carloni, Gabriele Varani, Giovanni Bussi. J Chem Theory Comput 2013
32
100

Development and current status of the CHARMM force field for nucleic acids.
A D MacKerell, N Banavali, N Foloppe. Biopolymers 2000
517
100

Imperfect CAG repeats form diverse structures in SCA1 transcripts.
Krzysztof Sobczak, Wlodzimierz J Krzyzosiak. J Biol Chem 2004
38
100

Translation of HTT mRNA with expanded CAG repeats is regulated by the MID1-PP2A protein complex.
Sybille Krauss, Nadine Griesche, Ewa Jastrzebska, Changwei Chen, Désiree Rutschow, Clemens Achmüller, Stephanie Dorn, Sylvia M Boesch, Maciej Lalowski, Erich Wanker,[...]. Nat Commun 2013
55
100

Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.
Alastair I H Murchie, Ben Davis, Catherine Isel, Mohammad Afshar, Martin J Drysdale, Justin Bower, Andrew J Potter, Ian D Starkey, Terry M Swarbrick, Shabana Mirza,[...]. J Mol Biol 2004
106
100

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
470
100

Targeting RNA with small molecules: from fundamental principles towards the clinic.
James P Falese, Anita Donlic, Amanda E Hargrove. Chem Soc Rev 2021
15
100

Selective small-molecule inhibition of an RNA structural element.
John A Howe, Hao Wang, Thierry O Fischmann, Carl J Balibar, Li Xiao, Andrew M Galgoci, Juliana C Malinverni, Todd Mayhood, Artjohn Villafania, Ali Nahvi,[...]. Nature 2015
193
100


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.