Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
Times Cited: 207
Times Cited: 207
Times Cited
Times Co-cited
Similarity
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
Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J Martin, Johannes Söding, Martin Steinegger. Nucleic Acids Res 2017
28
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
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
25
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
Martin Steinegger, Johannes Söding. Nat Biotechnol 2017
Martin Steinegger, Johannes Söding. Nat Biotechnol 2017
20
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
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
17
Clustering huge protein sequence sets in linear time.
Martin Steinegger, Johannes Söding. Nat Commun 2018
Martin Steinegger, Johannes Söding. Nat Commun 2018
16
BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
15
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
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
15
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
15
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
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
15
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
W Kabsch, C Sander. Biopolymers 1983
W Kabsch, C Sander. Biopolymers 1983
14
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
14
Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
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
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
13
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
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
13
CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
12
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
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
12
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
11
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Kazutaka Katoh, Daron M Standley. Mol Biol Evol 2013
Kazutaka Katoh, Daron M Standley. Mol Biol Evol 2013
11
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
11
10
TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
10
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
10
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
9
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
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
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
Baris E Suzek, Yuqi Wang, Hongzhan Huang, Peter B McGarvey, Cathy H Wu. Bioinformatics 2015
9
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
9
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.
Martin Steinegger, Milot Mirdita, Johannes Söding. Nat Methods 2019
Martin Steinegger, Milot Mirdita, Johannes Söding. Nat Methods 2019
15
Unified rational protein engineering with sequence-based deep representation learning.
Ethan C Alley, Grigory Khimulya, Surojit Biswas, Mohammed AlQuraishi, George M Church. Nat Methods 2019
Ethan C Alley, Grigory Khimulya, Surojit Biswas, Mohammed AlQuraishi, George M Church. Nat Methods 2019
9
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.
David T Jones, Tanya Singh, Tomasz Kosciolek, Stuart Tetchner. Bioinformatics 2015
David T Jones, Tanya Singh, Tomasz Kosciolek, Stuart Tetchner. Bioinformatics 2015
8
The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
8
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
Chengxin Zhang, Wei Zheng, S M Mortuza, Yang Li, Yang Zhang. Bioinformatics 2020
14
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
Robert C Edgar. Nucleic Acids Res 2004
7
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.
Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J Gray. Bioinformatics 2010
Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J Gray. Bioinformatics 2010
7
Modeling aspects of the language of life through transfer-learning protein sequences.
Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes, Burkhard Rost. BMC Bioinformatics 2019
Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes, Burkhard Rost. BMC Bioinformatics 2019
9
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
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
7
Critical assessment of methods of protein structure prediction (CASP)-Round XIII.
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
6
Fast and sensitive protein alignment using DIAMOND.
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
6
QMEANDisCo-distance constraints applied on model quality estimation.
Gabriel Studer, Christine Rempfer, Andrew M Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede. Bioinformatics 2020
Gabriel Studer, Christine Rempfer, Andrew M Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede. Bioinformatics 2020
6
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen,[...]. Nucleic Acids Res 2019
Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen,[...]. Nucleic Acids Res 2019
6
6
Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models.
Magnus Ekeberg, Cecilia Lövkvist, Yueheng Lan, Martin Weigt, Erik Aurell. Phys Rev E Stat Nonlin Soft Matter Phys 2013
Magnus Ekeberg, Cecilia Lövkvist, Yueheng Lan, Martin Weigt, Erik Aurell. Phys Rev E Stat Nonlin Soft Matter Phys 2013
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
Simon C Potter, Aurélien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez, Robert D Finn. Nucleic Acids Res 2018
6
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
CATH: increased structural coverage of functional space.
Ian Sillitoe, Nicola Bordin, Natalie Dawson, Vaishali P Waman, Paul Ashford, Harry M Scholes, Camilla S M Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen,[...]. Nucleic Acids Res 2021
Ian Sillitoe, Nicola Bordin, Natalie Dawson, Vaishali P Waman, Paul Ashford, Harry M Scholes, Camilla S M Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen,[...]. Nucleic Acids Res 2021
13
Identification of direct residue contacts in protein-protein interaction by message passing.
Martin Weigt, Robert A White, Hendrik Szurmant, James A Hoch, Terence Hwa. Proc Natl Acad Sci U S A 2009
Martin Weigt, Robert A White, Hendrik Szurmant, James A Hoch, Terence Hwa. Proc Natl Acad Sci U S A 2009
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.