Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
Times Cited: 1109
Times Cited: 1109
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
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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
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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
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Improved protein structure prediction using potentials from deep learning.
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BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
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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
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
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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
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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
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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
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu. PLoS Comput Biol 2017
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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
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UCSF Chimera--a visualization system for exploratory research and analysis.
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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Weizhong Li, Adam Godzik. Bioinformatics 2006
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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
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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
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
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CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations.
Stefan Seemayer, Markus Gruber, Johannes Söding. Bioinformatics 2014
Stefan Seemayer, Markus Gruber, Johannes Söding. Bioinformatics 2014
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DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins.
Chengxin Zhang, Wei Zheng, S M Mortuza, Yang Li, Yang Zhang. Bioinformatics 2020
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CD-HIT: accelerated for clustering the next-generation sequencing data.
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10
Toward the estimation of the absolute quality of individual protein structure models.
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
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Basic local alignment search tool.
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UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
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TM-align: a protein structure alignment algorithm based on the TM-score.
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Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.
Jack Hanson, Kuldip Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou. Bioinformatics 2018
Jack Hanson, Kuldip Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou. Bioinformatics 2018
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HMMER web server: interactive sequence similarity searching.
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WebLogo: a sequence logo generator.
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8
Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.
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8
Clustering huge protein sequence sets in linear time.
Martin Steinegger, Johannes Söding. Nat Commun 2018
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8
Scoring function for automated assessment of protein structure template quality.
Yang Zhang, Jeffrey Skolnick. Proteins 2004
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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
David T Jones, Daniel W A Buchan, Domenico Cozzetto, Massimiliano Pontil. Bioinformatics 2012
8
RaptorX-Property: a web server for protein structure property prediction.
Sheng Wang, Wei Li, Shiwang Liu, Jinbo Xu. Nucleic Acids Res 2016
Sheng Wang, Wei Li, Shiwang Liu, Jinbo Xu. Nucleic Acids Res 2016
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
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The HHpred interactive server for protein homology detection and structure prediction.
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The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
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7
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.
Martin Steinegger, Milot Mirdita, Johannes Söding. Nat Methods 2019
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Comparative protein modelling by satisfaction of spatial restraints.
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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.
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Hidden Markov model speed heuristic and iterative HMM search procedure.
L Steven Johnson, Sean R Eddy, Elon Portugaly. BMC Bioinformatics 2010
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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
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Distance-based protein folding powered by deep learning.
Jinbo Xu. Proc Natl Acad Sci U S A 2019
Jinbo Xu. Proc Natl Acad Sci U S A 2019
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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
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DNCON2: improved protein contact prediction using two-level deep convolutional neural networks.
Badri Adhikari, Jie Hou, Jianlin Cheng. Bioinformatics 2018
Badri Adhikari, Jie Hou, Jianlin Cheng. Bioinformatics 2018
6
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
Lawrence A Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J E Sternberg. Nat Protoc 2015
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MUSCLE: multiple sequence alignment with high accuracy and high throughput.
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Robert C Edgar. Nucleic Acids Res 2004
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HMMER web server: 2018 update.
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Simon C Potter, Aurélien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez, Robert D Finn. Nucleic Acids Res 2018
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
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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
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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
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
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.