A citation-based method for searching scientific literature

Hua Cheng, R Dustin Schaeffer, Yuxing Liao, Lisa N Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V Grishin. PLoS Comput Biol 2014
Times Cited: 158







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



Times Cited
  Times     Co-cited
Similarity



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
23

TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
22

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
21

CATH: an expanded resource to predict protein function through structure and sequence.
Natalie L Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, David Lee, Paul Ashford, Christine A Orengo, Ian Sillitoe. Nucleic Acids Res 2017
204
21


A vocabulary of ancient peptides at the origin of folded proteins.
Vikram Alva, Johannes Söding, Andrei N Lupas. Elife 2015
107
19

Protein homology detection by HMM-HMM comparison.
Johannes Söding. Bioinformatics 2005
18

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
17


Manual classification strategies in the ECOD database.
Hua Cheng, Yuxing Liao, R Dustin Schaeffer, Nick V Grishin. Proteins 2015
30
50


Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths.
Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny. Proc Natl Acad Sci U S A 2017
33
39

CATH--a hierarchic classification of protein domain structures.
C A Orengo, A D Michie, S Jones, D T Jones, M B Swindells, J M Thornton. Structure 1997
12

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures.
Antonina Andreeva, Eugene Kulesha, Julian Gough, Alexey G Murzin. Nucleic Acids Res 2020
63
19

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.
Lukas Zimmermann, Andrew Stephens, Seung-Zin Nam, David Rau, Jonas Kübler, Marko Lozajic, Felix Gabler, Johannes Söding, Andrei N Lupas, Vikram Alva. J Mol Biol 2018
958
11


Simple yet functional phosphate-loop proteins.
Maria Luisa Romero Romero, Fan Yang, Yu-Ru Lin, Agnes Toth-Petroczy, Igor N Berezovsky, Alexander Goncearenco, Wen Yang, Alon Wellner, Fanindra Kumar-Deshmukh, Michal Sharon,[...]. Proc Natl Acad Sci U S A 2018
34
32

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
10


ECOD: new developments in the evolutionary classification of domains.
R Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V Grishin. Nucleic Acids Res 2017
31
32

An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors.
Paola Laurino, Ágnes Tóth-Petróczy, Rubén Meana-Pañeda, Wei Lin, Donald G Truhlar, Dan S Tawfik. PLoS Biol 2016
48
20

The Pfam protein families database in 2019.
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019
10

Improved protein structure prediction using potentials from deep learning.
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Nature 2020
667
10

Protein structure determination using metagenome sequence data.
Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A Pavlopoulos, David E Kim, Hetunandan Kamisetty, Nikos C Kyrpides, David Baker. Science 2017
266
9


Global view of the protein universe.
Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny. Proc Natl Acad Sci U S A 2014
44
20


A galaxy of folds.
Vikram Alva, Michael Remmert, Andreas Biegert, Andrei N Lupas, Johannes Söding. Protein Sci 2010
52
17


Dali server update.
Liisa Holm, Laura M Laakso. Nucleic Acids Res 2016
604
9

HH-suite3 for fast remote homology detection and deep protein annotation.
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
178
9




Evolutionary relationship of two ancient protein superfolds.
José Arcadio Farías-Rico, Steffen Schmidt, Birte Höcker. Nat Chem Biol 2014
40
20

SCOP2 prototype: a new approach to protein structure mining.
Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey G Murzin. Nucleic Acids Res 2014
155
8


Accelerated Profile HMM Searches.
Sean R Eddy. PLoS Comput Biol 2011
8

The Pfam protein families database: towards a more sustainable future.
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas,[...]. Nucleic Acids Res 2016
8


The HHpred interactive server for protein homology detection and structure prediction.
Johannes Söding, Andreas Biegert, Andrei N Lupas. Nucleic Acids Res 2005
7

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.
Valerio Mariani, Marco Biasini, Alessandro Barbato, Torsten Schwede. Bioinformatics 2013
147
7

PISCES: a protein sequence culling server.
Guoli Wang, Roland L Dunbrack. Bioinformatics 2003
7


Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
7

CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Ian Sillitoe, Natalie Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, Paul Ashford, Adeyelu Tolulope, Harry M Scholes, Ilya Senatorov, Andra Bujan,[...]. Nucleic Acids Res 2019
69
10

Critical assessment of methods of protein structure prediction (CASP)-Round XIII.
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
173
7

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
7

CASP11 statistics and the prediction center evaluation system.
Andriy Kryshtafovych, Bohdan Monastyrskyy, Krzysztof Fidelis. Proteins 2016
29
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.