A citation-based method for searching scientific literature

Sneha Vishwanath, Alexandre G de Brevern, Narayanaswamy Srinivasan. PLoS Comput Biol 2018
Times Cited: 22







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



Times Cited
  Times     Co-cited
Similarity


The folding and evolution of multidomain proteins.
Jung-Hoon Han, Sarah Batey, Adrian A Nickson, Sarah A Teichmann, Jane Clarke. Nat Rev Mol Cell Biol 2007
250
22

Stability of domain structures in multi-domain proteins.
Ramachandra M Bhaskara, Narayanaswamy Srinivasan. Sci Rep 2011
65
22

Domain combinations in archaeal, eubacterial and eukaryotic proteomes.
G Apic, J Gough, S A Teichmann. J Mol Biol 2001
339
22

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
22


PIC: Protein Interactions Calculator.
K G Tina, R Bhadra, N Srinivasan. Nucleic Acids Res 2007
638
13


Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions.
Diana Ekman, Asa K Björklund, Johannes Frey-Skött, Arne Elofsson. J Mol Biol 2005
152
13

The multiplicity of domains in proteins.
R F Doolittle. Annu Rev Biochem 1995
380
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
13

The anatomy and taxonomy of protein structure.
J S Richardson. Adv Protein Chem 1981
13

Studying the folding of multidomain proteins.
Sarah Batey, Adrian A Nickson, Jane Clarke. HFSP J 2008
56
13

Fusion protein linkers: property, design and functionality.
Xiaoying Chen, Jennica L Zaro, Wei-Chiang Shen. Adv Drug Deliv Rev 2013
786
13

Principles for designing ideal protein structures.
Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Rong Xiao, Thomas B Acton, Gaetano T Montelione, David Baker. Nature 2012
336
13

TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
13

Structure, function and evolution of multidomain proteins.
Christine Vogel, Matthew Bashton, Nicola D Kerrison, Cyrus Chothia, Sarah A Teichmann. Curr Opin Struct Biol 2004
270
13

Allostery and cooperativity revisited.
Qiang Cui, Martin Karplus. Protein Sci 2008
471
9

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.
J MONOD, J WYMAN, J P CHANGEUX. J Mol Biol 1965
9

Using chemical shift perturbation to characterise ligand binding.
Mike P Williamson. Prog Nucl Magn Reson Spectrosc 2013
769
9

Networks of Dynamic Allostery Regulate Enzyme Function.
Michael Joseph Holliday, Carlo Camilloni, Geoffrey Stuart Armstrong, Michele Vendruscolo, Elan Zohar Eisenmesser. Structure 2017
41
9

A unified view of "how allostery works".
Chung-Jung Tsai, Ruth Nussinov. PLoS Comput Biol 2014
246
9

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.
Elena Papaleo, Giorgio Saladino, Matteo Lambrughi, Kresten Lindorff-Larsen, Francesco Luigi Gervasio, Ruth Nussinov. Chem Rev 2016
206
9



Evolution of protein domain promiscuity in eukaryotes.
Malay Kumar Basu, Liran Carmel, Igor B Rogozin, Eugene V Koonin. Genome Res 2008
127
9

How do new proteins arise?
Erich Bornberg-Bauer, Ann-Kathrin Huylmans, Tobias Sikosek. Curr Opin Struct Biol 2010
47
9

Dynamic allostery: linkers are not merely flexible.
Buyong Ma, Chung-Jung Tsai, Türkan Haliloğlu, Ruth Nussinov. Structure 2011
166
9

The relationship between domain duplication and recombination.
Christine Vogel, Sarah A Teichmann, Jose Pereira-Leal. J Mol Biol 2005
123
9


Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.
Raju Kalaivani, Raju Reema, Narayanaswamy Srinivasan. PLoS Comput Biol 2018
3
66

CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
9

Domain insertion permissibility-guided engineering of allostery in ion channels.
Willow Coyote-Maestas, Yungui He, Chad L Myers, Daniel Schmidt. Nat Commun 2019
12
16

Evolution of the human ion channel set.
Timothy J Jegla, Christian M Zmasek, Serge Batalov, Surendra K Nayak. Comb Chem High Throughput Screen 2009
67
9

Global analysis of protein folding using massively parallel design, synthesis, and testing.
Gabriel J Rocklin, Tamuka M Chidyausiku, Inna Goreshnik, Alex Ford, Scott Houliston, Alexander Lemak, Lauren Carter, Rashmi Ravichandran, Vikram K Mulligan, Aaron Chevalier,[...]. Science 2017
200
9

Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.
Benjamin L Oakes, Dana C Nadler, Avi Flamholz, Christof Fellmann, Brett T Staahl, Jennifer A Doudna, David F Savage. Nat Biotechnol 2016
119
9

Designing switchable enzymes.
Marc Ostermeier. Curr Opin Struct Biol 2009
56
9

Inwardly rectifying potassium channels: their structure, function, and physiological roles.
Hiroshi Hibino, Atsushi Inanobe, Kazuharu Furutani, Shingo Murakami, Ian Findlay, Yoshihisa Kurachi. Physiol Rev 2010
951
9

Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis.
Joshua T Atkinson, Alicia M Jones, Quan Zhou, Jonathan J Silberg. Nucleic Acids Res 2018
11
18

Determining protein structures using deep mutagenesis.
Jörn M Schmiedel, Ben Lehner. Nat Genet 2019
68
9

Golgi export of the Kir2.1 channel is driven by a trafficking signal located within its tertiary structure.
Donghui Ma, Tarvinder Kaur Taneja, Brian M Hagen, Bo-Young Kim, Bernardo Ortega, W Jonathan Lederer, Paul A Welling. Cell 2011
76
9

Deep mutational scanning: a new style of protein science.
Douglas M Fowler, Stanley Fields. Nat Methods 2014
478
9

Design of protein switches based on an ensemble model of allostery.
Jay H Choi, Abigail H Laurent, Vincent J Hilser, Marc Ostermeier. Nat Commun 2015
53
9

Multiplex assessment of protein variant abundance by massively parallel sequencing.
Kenneth A Matreyek, Lea M Starita, Jason J Stephany, Beth Martin, Melissa A Chiasson, Vanessa E Gray, Martin Kircher, Arineh Khechaduri, Jennifer N Dines, Ronald J Hause,[...]. Nat Genet 2018
157
9

The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gating.
Katherine Fallen, Sreedatta Banerjee, Jonathan Sheehan, Daniel Addison, L Michelle Lewis, Jens Meiler, Jerod S Denton. Channels (Austin) 2009
19
10

Genetically encoded indicators of neuronal activity.
Michael Z Lin, Mark J Schnitzer. Nat Neurosci 2016
330
9

Engineering extrinsic disorder to control protein activity in living cells.
Onur Dagliyan, Miroslaw Tarnawski, Pei-Hsuan Chu, David Shirvanyants, Ilme Schlichting, Nikolay V Dokholyan, Klaus M Hahn. Science 2016
129
9

Surface sites for engineering allosteric control in proteins.
Jeeyeon Lee, Madhusudan Natarajan, Vishal C Nashine, Michael Socolich, Tina Vo, William P Russ, Stephen J Benkovic, Rama Ranganathan. Science 2008
252
9


The language of the protein universe.
Andrea Scaiewicz, Michael Levitt. Curr Opin Genet Dev 2015
18
11


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.