A citation-based method for searching scientific literature

Ayush Jhunjhunwala, Zakir Ali, Sohini Bhattacharya, Antarip Halder, Abhijit Mitra, Purshotam Sharma. J Chem Inf Model 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
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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
50

Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
Keith A Corbino, Jeffrey E Barrick, Jinsoo Lim, Rüdiger Welz, Brian J Tucker, Izabela Puskarz, Maumita Mandal, Noam D Rudnick, Ronald R Breaker. Genome Biol 2005
168
50

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
Zasha Weinberg, Elizabeth E Regulski, Ming C Hammond, Jeffrey E Barrick, Zizhen Yao, Walter L Ruzzo, Ronald R Breaker. RNA 2008
76
50


Structure of the Guanidine III Riboswitch.
Lin Huang, Jia Wang, Timothy J Wilson, David M J Lilley. Cell Chem Biol 2017
29
50

CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs.
Thomas Giannos, Samo Lešnik, Urban Bren, Milan Hodošček, Tatiana Domratcheva, Ana-Nicoleta Bondar. J Chem Inf Model 2021
2
50

Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.
Caroline W Reiss, Yong Xiong, Scott A Strobel. Structure 2017
40
50

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers.
Teresa Fornaro, Malgorzata Biczysko, Susanna Monti, Vincenzo Barone. Phys Chem Chem Phys 2014
42
50

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
50

W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model.
Michal Janeček, Petra Kührová, Vojtěch Mlýnský, Michal Otyepka, Jiří Šponer, Pavel Banáš. J Chem Theory Comput 2021
2
50

Potential Energy Function for Fentanyl-Based Opioid Pain Killers.
Samo Lešnik, Milan Hodošček, Urban Bren, Christoph Stein, Ana-Nicoleta Bondar. J Chem Inf Model 2020
7
50

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class.
James W Nelson, Ruben M Atilho, Madeline E Sherlock, Randy B Stockbridge, Ronald R Breaker. Mol Cell 2017
74
50

Methods and Applications of In Silico Aptamer Design and Modeling.
Andrey A Buglak, Alexey V Samokhvalov, Anatoly V Zherdev, Boris B Dzantiev. Int J Mol Sci 2020
15
50



A broad-specificity multidrug efflux pump requiring a pair of homologous SMR-type proteins.
D L Jack, M L Storms, J H Tchieu, I T Paulsen, M H Saier. J Bacteriol 2000
79
50

Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations.
Arnost Mládek, Purshotam Sharma, Abhijit Mitra, Dhananjay Bhattacharyya, Jirí Sponer, Judit E Sponer. J Phys Chem B 2009
38
50

Riboswitch diversity and distribution.
Phillip J McCown, Keith A Corbino, Shira Stav, Madeline E Sherlock, Ronald R Breaker. RNA 2017
192
50

A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria.
Elena Poiata, Michelle M Meyer, Tyler D Ames, Ronald R Breaker. RNA 2009
70
50


A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain.
Adam Roth, Wade C Winkler, Elizabeth E Regulski, Bobby W K Lee, Jinsoo Lim, Inbal Jona, Jeffrey E Barrick, Ankita Ritwik, Jane N Kim, Rüdiger Welz,[...]. Nat Struct Mol Biol 2007
159
50

In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.
David R Bell, Jeffrey K Weber, Wang Yin, Tien Huynh, Wei Duan, Ruhong Zhou. Proc Natl Acad Sci U S A 2020
14
50

A decade of riboswitches.
Alexander Serganov, Evgeny Nudler. Cell 2013
594
50

An allosteric self-splicing ribozyme triggered by a bacterial second messenger.
Elaine R Lee, Jenny L Baker, Zasha Weinberg, Narasimhan Sudarsan, Ronald R Breaker. Science 2010
234
50


Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria.
Michelle M Meyer, Adam Roth, Stephanie M Chervin, George A Garcia, Ronald R Breaker. RNA 2008
76
50


Influence of the Number, Nature and Position of Methyl Posttranscriptional Modifications on Nucleobase Stacking in RNA.
Deepika Kagra, Amanpreet Singh Mahmi, N V Suresh Kumar, Preethi Seelam Prabhakar, Purshotam Sharma. Chemphyschem 2021
2
50

New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
Jeffrey E Barrick, Keith A Corbino, Wade C Winkler, Ali Nahvi, Maumita Mandal, Jennifer Collins, Mark Lee, Adam Roth, Narasimhan Sudarsan, Inbal Jona,[...]. Proc Natl Acad Sci U S A 2004
336
50



Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?
M Krepl, M Havrila, P Stadlbauer, P Banas, M Otyepka, J Pasulka, R Stefl, J Sponer. J Chem Theory Comput 2015
41
50


Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.
Brooke A Murphy McDaniel, Frank J Grundy, Irina Artsimovitch, Tina M Henkin. Proc Natl Acad Sci U S A 2003
191
50

Structural basis for guanidine sensing by the ykkC family of riboswitches.
Robert A Battaglia, Ian R Price, Ailong Ke. RNA 2017
33
50


Regulation of bacterial gene expression by riboswitches.
Wade C Winkler, Ronald R Breaker. Annu Rev Microbiol 2005
497
50


Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes.
Phillip J McCown, Jonathan J Liang, Zasha Weinberg, Ronald R Breaker. Chem Biol 2014
51
50

Riboswitches: structures and mechanisms.
Andrew D Garst, Andrea L Edwards, Robert T Batey. Cold Spring Harb Perspect Biol 2011
184
50

Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes.
Eugene Baulin, Valeriy Metelev, Alexey Bogdanov. Nucleic Acids Res 2020
1
100

Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch.
Gorle Suresh, Harini Srinivasan, Shivani Nanda, U Deva Priyakumar. Biochemistry 2016
5
50


Riboswitches in eubacteria sense the second messenger cyclic di-GMP.
N Sudarsan, E R Lee, Z Weinberg, R H Moy, J N Kim, K H Link, R R Breaker. Science 2008
456
50

TPP riboswitch aptamer: Role of Mg2+ ions, ligand unbinding, and allostery.
Siladitya Padhi, Meenakshi Pradhan, Navneet Bung, Arijit Roy, Gopalakrishnan Bulusu. J Mol Graph Model 2019
2
50

Molecular dynamics simulation on the allosteric analysis of the c-di-GMP class I riboswitch induced by ligand binding.
Chaoqun Li, Xiaojia Zhao, Pengtao Xie, Junping Hu, Huimin Bi. J Mol Recognit 2019
4
50

Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study.
Karan Deep Sharma, Preetleen Kathuria, Stacey D Wetmore, Purshotam Sharma. Phys Chem Chem Phys 2020
2
50


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.