A citation-based method for searching scientific literature

Khanh Dao Duc, Sanjit S Batra, Nicholas Bhattacharya, Jamie H D Cate, Yun S Song. Nucleic Acids Res 2019
Times Cited: 29







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



Times Cited
  Times     Co-cited
Similarity


The geometry of the ribosomal polypeptide exit tunnel.
N R Voss, M Gerstein, T A Steitz, P B Moore. J Mol Biol 2006
209
34

Cotranslational Protein Folding inside the Ribosome Exit Tunnel.
Ola B Nilsson, Rickard Hedman, Jacopo Marino, Stephan Wickles, Lukas Bischoff, Magnus Johansson, Annika Müller-Lucks, Fabio Trovato, Joseph D Puglisi, Edward P O'Brien,[...]. Cell Rep 2015
136
34

Folding zones inside the ribosomal exit tunnel.
Jianli Lu, Carol Deutsch. Nat Struct Mol Biol 2005
170
27

The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.
Renuka Kudva, Pengfei Tian, Fátima Pardo-Avila, Marta Carroni, Robert B Best, Harris D Bernstein, Gunnar von Heijne. Elife 2018
26
30

Cotranslational protein folding on the ribosome monitored in real time.
Wolf Holtkamp, Goran Kokic, Marcus Jäger, Joerg Mittelstaet, Anton A Komar, Marina V Rodnina. Science 2015
115
27

Arrest peptides: cis-acting modulators of translation.
Koreaki Ito, Shinobu Chiba. Annu Rev Biochem 2013
135
24

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
N Ban, P Nissen, J Hansen, P B Moore, T A Steitz. Science 2000
24

Translation regulation via nascent polypeptide-mediated ribosome stalling.
Daniel N Wilson, Stefan Arenz, Roland Beckmann. Curr Opin Struct Biol 2016
83
20

One core, two shells: bacterial and eukaryotic ribosomes.
Sergey Melnikov, Adam Ben-Shem, Nicolas Garreau de Loubresse, Lasse Jenner, Gulnara Yusupova, Marat Yusupov. Nat Struct Mol Biol 2012
222
20

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.
Ting Su, Jingdong Cheng, Daniel Sohmen, Rickard Hedman, Otto Berninghausen, Gunnar von Heijne, Daniel N Wilson, Roland Beckmann. Elife 2017
36
20

Structure of the 70S ribosome complexed with mRNA and tRNA.
Maria Selmer, Christine M Dunham, Frank V Murphy, Albert Weixlbaumer, Sabine Petry, Ann C Kelley, John R Weir, V Ramakrishnan. Science 2006
935
20


Tertiary interactions within the ribosomal exit tunnel.
Andrey Kosolapov, Carol Deutsch. Nat Struct Mol Biol 2009
91
20

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding.
Gong Zhang, Magdalena Hubalewska, Zoya Ignatova. Nat Struct Mol Biol 2009
373
20

Cotranslational Folding of Proteins on the Ribosome.
Marija Liutkute, Ekaterina Samatova, Marina V Rodnina. Biomolecules 2020
25
24

Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.
Wenfei Li, Fred R Ward, Kim F McClure, Stacey Tsai-Lan Chang, Elizabeth Montabana, Spiros Liras, Robert G Dullea, Jamie H D Cate. Nat Struct Mol Biol 2019
23
21

alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
Shashi Bhushan, Marco Gartmann, Mario Halic, Jean-Paul Armache, Alexander Jarasch, Thorsten Mielke, Otto Berninghausen, Daniel N Wilson, Roland Beckmann. Nat Struct Mol Biol 2010
134
17


The structural basis of ribosome activity in peptide bond synthesis.
P Nissen, J Hansen, N Ban, P B Moore, T A Steitz. Science 2000
17

The ribosome modulates nascent protein folding.
Christian M Kaiser, Daniel H Goldman, John D Chodera, Ignacio Tinoco, Carlos Bustamante. Science 2011
174
17

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations.
Florian Buhr, Sujata Jha, Michael Thommen, Joerg Mittelstaet, Felicitas Kutz, Harald Schwalbe, Marina V Rodnina, Anton A Komar. Mol Cell 2016
154
17

Cotranslational folding of spectrin domains via partially structured states.
Ola B Nilsson, Adrian A Nickson, Jeffrey J Hollins, Stephan Wickles, Annette Steward, Roland Beckmann, Gunnar von Heijne, Jane Clarke. Nat Struct Mol Biol 2017
53
17

Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome.
José Arcadio Farías-Rico, Frida Ruud Selin, Ioanna Myronidi, Marie Frühauf, Gunnar von Heijne. Proc Natl Acad Sci U S A 2018
31
17

Ribosome exit tunnel can entropically stabilize alpha-helices.
Guy Ziv, Gilad Haran, D Thirumalai. Proc Natl Acad Sci U S A 2005
102
17

Protein folding at the exit tunnel.
Daria V Fedyukina, Silvia Cavagnero. Annu Rev Biophys 2011
64
17

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts.
Petr Tesina, Laura N Lessen, Robert Buschauer, Jingdong Cheng, Colin Chih-Chien Wu, Otto Berninghausen, Allen R Buskirk, Thomas Becker, Roland Beckmann, Rachel Green. EMBO J 2020
42
17

Mechanism of ribosome stalling during translation of a poly(A) tail.
Viswanathan Chandrasekaran, Szymon Juszkiewicz, Junhong Choi, Joseph D Puglisi, Alan Brown, Sichen Shao, V Ramakrishnan, Ramanujan S Hegde. Nat Struct Mol Biol 2019
44
17

How Macrolide Antibiotics Work.
Nora Vázquez-Laslop, Alexander S Mankin. Trends Biochem Sci 2018
63
17



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
17

Positively charged residues are the major determinants of ribosomal velocity.
Catherine A Charneski, Laurence D Hurst. PLoS Biol 2013
171
13

Transmembrane but not soluble helices fold inside the ribosome tunnel.
Manuel Bañó-Polo, Carlos Baeza-Delgado, Silvia Tamborero, Anthony Hazel, Brayan Grau, IngMarie Nilsson, Paul Whitley, James C Gumbart, Gunnar von Heijne, Ismael Mingarro. Nat Commun 2018
13
30

Co-Translational Folding Trajectory of the HemK Helical Domain.
Evan Mercier, Marina V Rodnina. Biochemistry 2018
16
25

Structural characterization of the interaction of α-synuclein nascent chains with the ribosomal surface and trigger factor.
Annika Deckert, Christopher A Waudby, Tomasz Wlodarski, Anne S Wentink, Xiaolin Wang, John P Kirkpatrick, Jack F S Paton, Carlo Camilloni, Predrag Kukic, Christopher M Dobson,[...]. Proc Natl Acad Sci U S A 2016
32
13

Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics.
Anders M Knight, Peter H Culviner, Neşe Kurt-Yilmaz, Taisong Zou, S Banu Ozkan, Silvia Cavagnero. ACS Chem Biol 2013
48
13


Folding pathway of an Ig domain is conserved on and off the ribosome.
Pengfei Tian, Annette Steward, Renuka Kudva, Ting Su, Patrick J Shilling, Adrian A Nickson, Jeffrey J Hollins, Roland Beckmann, Gunnar von Heijne, Jane Clarke,[...]. Proc Natl Acad Sci U S A 2018
43
13

Structures of the bacterial ribosome at 3.5 A resolution.
Barbara S Schuwirth, Maria A Borovinskaya, Cathy W Hau, Wen Zhang, Antón Vila-Sanjurjo, James M Holton, Jamie H Doudna Cate. Science 2005
969
13

Structural analysis of a signal peptide inside the ribosome tunnel by DNP MAS NMR.
Sascha Lange, W Trent Franks, Nandhakishore Rajagopalan, Kristina Döring, Michel A Geiger, Arne Linden, Barth-Jan van Rossum, Günter Kramer, Bernd Bukau, Hartmut Oschkinat. Sci Adv 2016
23
17

A structural ensemble of a ribosome-nascent chain complex during cotranslational protein folding.
Lisa D Cabrita, AnaÏs M E Cassaignau, Helene M M Launay, Christopher A Waudby, Tomasz Wlodarski, Carlo Camilloni, Maria-Evangelia Karyadi, Amy L Robertson, Xiaolin Wang, Anne S Wentink,[...]. Nat Struct Mol Biol 2016
80
13

Transient tertiary structure formation within the ribosome exit port.
Edward P O'Brien, Shang-Te Danny Hsu, John Christodoulou, Michele Vendruscolo, Christopher M Dobson. J Am Chem Soc 2010
56
13

Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors.
Rodrigo D Requião, Henrique José Araujo de Souza, Silvana Rossetto, Tatiana Domitrovic, Fernando L Palhano. RNA Biol 2016
25
16

Small protein domains fold inside the ribosome exit tunnel.
Jacopo Marino, Gunnar von Heijne, Roland Beckmann. FEBS Lett 2016
43
13

A new system for naming ribosomal proteins.
Nenad Ban, Roland Beckmann, Jamie H D Cate, Jonathan D Dinman, François Dragon, Steven R Ellis, Denis L J Lafontaine, Lasse Lindahl, Anders Liljas, Jeffrey M Lipton,[...]. Curr Opin Struct Biol 2014
315
13

Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution.
Jean-Paul Armache, Andreas M Anger, Viter Márquez, Sibylle Franckenberg, Thomas Fröhlich, Elizabeth Villa, Otto Berninghausen, Michael Thomm, Georg J Arnold, Roland Beckmann,[...]. Nucleic Acids Res 2013
44
13

Structural Patching Fosters Divergence of Mitochondrial Ribosomes.
Anton S Petrov, Elizabeth C Wood, Chad R Bernier, Ashlyn M Norris, Alan Brown, Alexey Amunts. Mol Biol Evol 2019
26
15

Ribosomes slide on lysine-encoding homopolymeric A stretches.
Kristin S Koutmou, Anthony P Schuller, Julie L Brunelle, Aditya Radhakrishnan, Sergej Djuranovic, Rachel Green. Elife 2015
65
13

Ribosome-associated protein quality control.
Onn Brandman, Ramanujan S Hegde. Nat Struct Mol Biol 2016
216
13

Revising the Structural Diversity of Ribosomal Proteins Across the Three Domains of Life.
Sergey Melnikov, Kasidet Manakongtreecheep, Dieter Söll. Mol Biol Evol 2018
29
13


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.