A citation-based method for searching scientific literature

Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
Times Cited: 1109







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



Times Cited
  Times     Co-cited
Similarity


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
35

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
28

Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J Martin, Johannes Söding, Martin Steinegger. Nucleic Acids Res 2017
185
26

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
754
20

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
19

Improved protein structure prediction using predicted interresidue orientations.
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
449
17

SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
16


Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu. PLoS Comput Biol 2017
416
14

Protein homology detection by HMM-HMM comparison.
Johannes Söding. Bioinformatics 2005
14

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
512
14

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 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
12

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
229
12

CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations.
Stefan Seemayer, Markus Gruber, Johannes Söding. Bioinformatics 2014
220
11

Accelerated Profile HMM Searches.
Sean R Eddy. PLoS Comput Biol 2011
10


CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
10

Toward the estimation of the absolute quality of individual protein structure models.
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
10

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
9

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
Baris E Suzek, Yuqi Wang, Hongzhan Huang, Peter B McGarvey, Cathy H Wu. Bioinformatics 2015
527
9

TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
9


HMMER web server: interactive sequence similarity searching.
Robert D Finn, Jody Clements, Sean R Eddy. Nucleic Acids Res 2011
8

WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
8


Clustering huge protein sequence sets in linear time.
Martin Steinegger, Johannes Söding. Nat Commun 2018
165
8


PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments.
David T Jones, Daniel W A Buchan, Domenico Cozzetto, Massimiliano Pontil. Bioinformatics 2012
464
8

RaptorX-Property: a web server for protein structure property prediction.
Sheng Wang, Wei Li, Shiwang Liu, Jinbo Xu. Nucleic Acids Res 2016
219
7

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning.
Michael Schantz Klausen, Martin Closter Jespersen, Henrik Nielsen, Kamilla Kjaergaard Jensen, Vanessa Isabell Jurtz, Casper Kaae Sønderby, Morten Otto Alexander Sommer, Ole Winther, Morten Nielsen, Bent Petersen,[...]. Proteins 2019
169
7

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


The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
7

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.
Martin Steinegger, Milot Mirdita, Johannes Söding. Nat Methods 2019
63
11


Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.
Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C Lawrence Zitnick, Jerry Ma,[...]. Proc Natl Acad Sci U S A 2021
140
7

Hidden Markov model speed heuristic and iterative HMM search procedure.
L Steven Johnson, Sean R Eddy, Elon Portugaly. BMC Bioinformatics 2010
493
7

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.
Hetunandan Kamisetty, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2013
383
7

Distance-based protein folding powered by deep learning.
Jinbo Xu. Proc Natl Acad Sci U S A 2019
162
7

Highly accurate protein structure prediction for the human proteome.
Kathryn Tunyasuvunakool, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon,[...]. Nature 2021
398
7


PISCES: a protein sequence culling server.
Guoli Wang, Roland L Dunbrack. Bioinformatics 2003
6

The Phyre2 web portal for protein modeling, prediction and analysis.
Lawrence A Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J E Sternberg. Nat Protoc 2015
6


HMMER web server: 2018 update.
Simon C Potter, Aurélien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez, Robert D Finn. Nucleic Acids Res 2018
562
6

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.
Marco Biasini, Stefan Bienert, Andrew Waterhouse, Konstantin Arnold, Gabriel Studer, Tobias Schmidt, Florian Kiefer, Tiziano Gallo Cassarino, Martino Bertoni, Lorenza Bordoli,[...]. Nucleic Acids Res 2014
6

ProtTrans: Towards Cracking the Language of Lifes Code Through Self-Supervised Deep Learning and High Performance Computing.
Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rehawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger,[...]. IEEE Trans Pattern Anal Mach Intell 2021
66
9

Direct-coupling analysis of residue coevolution captures native contacts across many protein families.
Faruck Morcos, Andrea Pagnani, Bryan Lunt, Arianna Bertolino, Debora S Marks, Chris Sander, Riccardo Zecchina, José N Onuchic, Terence Hwa, Martin Weigt. Proc Natl Acad Sci U S A 2011
698
6


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.