Marco Biasini, Stefan Bienert, Andrew Waterhouse, Konstantin Arnold, Gabriel Studer, Tobias Schmidt, Florian Kiefer, Tiziano Gallo Cassarino, Martino Bertoni, Lorenza Bordoli, Torsten Schwede. Nucleic Acids Res 2014
Times Cited: 2984
Times Cited: 2984
Times Cited
Times Co-cited
Similarity
Toward the estimation of the absolute quality of individual protein structure models.
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
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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
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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
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
17
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp, Torsten Schwede. Bioinformatics 2006
Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp, Torsten Schwede. Bioinformatics 2006
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Verification of protein structures: patterns of nonbonded atomic interactions.
C Colovos, T O Yeates. Protein Sci 1993
C Colovos, T O Yeates. Protein Sci 1993
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ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.
Markus Wiederstein, Manfred J Sippl. Nucleic Acids Res 2007
Markus Wiederstein, Manfred J Sippl. Nucleic Acids Res 2007
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
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QMEAN: A comprehensive scoring function for model quality assessment.
Pascal Benkert, Silvio C E Tosatto, Dietmar Schomburg. Proteins 2008
Pascal Benkert, Silvio C E Tosatto, Dietmar Schomburg. Proteins 2008
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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
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PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Paul D Adams, Pavel V Afonine, Gábor Bunkóczi, Vincent B Chen, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Li-Wei Hung, Gary J Kapral, Ralf W Grosse-Kunstleve,[...]. Acta Crystallogr D Biol Crystallogr 2010
Paul D Adams, Pavel V Afonine, Gábor Bunkóczi, Vincent B Chen, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Li-Wei Hung, Gary J Kapral, Ralf W Grosse-Kunstleve,[...]. Acta Crystallogr D Biol Crystallogr 2010
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SWISS-MODEL: An automated protein homology-modeling server.
Torsten Schwede, Jürgen Kopp, Nicolas Guex, Manuel C Peitsch. Nucleic Acids Res 2003
Torsten Schwede, Jürgen Kopp, Nicolas Guex, Manuel C Peitsch. Nucleic Acids Res 2003
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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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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
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Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
K J Livak, T D Schmittgen. Methods 2001
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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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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
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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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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
5
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
5
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
5
SignalP 5.0 improves signal peptide predictions using deep neural networks.
José Juan Almagro Armenteros, Konstantinos D Tsirigos, Casper Kaae Sønderby, Thomas Nordahl Petersen, Ole Winther, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Biotechnol 2019
José Juan Almagro Armenteros, Konstantinos D Tsirigos, Casper Kaae Sønderby, Thomas Nordahl Petersen, Ole Winther, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Biotechnol 2019
5
Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
5
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
4
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
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QMEAN server for protein model quality estimation.
Pascal Benkert, Michael Künzli, Torsten Schwede. Nucleic Acids Res 2009
Pascal Benkert, Michael Künzli, Torsten Schwede. Nucleic Acids Res 2009
4
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology.
Martino Bertoni, Florian Kiefer, Marco Biasini, Lorenza Bordoli, Torsten Schwede. Sci Rep 2017
Martino Bertoni, Florian Kiefer, Marco Biasini, Lorenza Bordoli, Torsten Schwede. Sci Rep 2017
4
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
4
The carbohydrate-active enzymes database (CAZy) in 2013.
Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M Coutinho, Bernard Henrissat. Nucleic Acids Res 2014
Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M Coutinho, Bernard Henrissat. Nucleic Acids Res 2014
4
Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
4
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
4
Deciphering key features in protein structures with the new ENDscript server.
Xavier Robert, Patrice Gouet. Nucleic Acids Res 2014
Xavier Robert, Patrice Gouet. Nucleic Acids Res 2014
4
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, Sudhir Kumar. Mol Biol Evol 2013
Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, Sudhir Kumar. Mol Biol Evol 2013
4
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
N Saitou, M Nei. Mol Biol Evol 1987
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4
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
Robert C Edgar. Nucleic Acids Res 2004
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Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.
Nicolas Guex, Manuel C Peitsch, Torsten Schwede. Electrophoresis 2009
Nicolas Guex, Manuel C Peitsch, Torsten Schwede. Electrophoresis 2009
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AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
Oleg Trott, Arthur J Olson. J Comput Chem 2010
Oleg Trott, Arthur J Olson. J Comput Chem 2010
4
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
4
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
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Phaser crystallographic software.
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
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CHARMM36m: an improved force field for folded and intrinsically disordered proteins.
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
4
mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Douglas E V Pires, David B Ascher, Tom L Blundell. Bioinformatics 2014
Douglas E V Pires, David B Ascher, Tom L Blundell. Bioinformatics 2014
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Open Babel: An open chemical toolbox.
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison. J Cheminform 2011
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison. J Cheminform 2011
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Contribution of hydrogen bonds to protein stability.
C Nick Pace, Hailong Fu, Katrina Lee Fryar, John Landua, Saul R Trevino, David Schell, Richard L Thurlkill, Satoshi Imura, J Martin Scholtz, Ketan Gajiwala,[...]. Protein Sci 2014
C Nick Pace, Hailong Fu, Katrina Lee Fryar, John Landua, Saul R Trevino, David Schell, Richard L Thurlkill, Satoshi Imura, J Martin Scholtz, Ketan Gajiwala,[...]. Protein Sci 2014
3
Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
Simon C Lovell, Ian W Davis, W Bryan Arendall, Paul I W de Bakker, J Michael Word, Michael G Prisant, Jane S Richardson, David C Richardson. Proteins 2003
Simon C Lovell, Ian W Davis, W Bryan Arendall, Paul I W de Bakker, J Michael Word, Michael G Prisant, Jane S Richardson, David C Richardson. Proteins 2003
3
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
3
Prediction of protein stability changes for single-site mutations using support vector machines.
Jianlin Cheng, Arlo Randall, Pierre Baldi. Proteins 2006
Jianlin Cheng, Arlo Randall, Pierre Baldi. Proteins 2006
3
Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
3
3Drefine: an interactive web server for efficient protein structure refinement.
Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng. Nucleic Acids Res 2016
Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng. Nucleic Acids Res 2016
3
Structural basis of receptor recognition by SARS-CoV-2.
Jian Shang, Gang Ye, Ke Shi, Yushun Wan, Chuming Luo, Hideki Aihara, Qibin Geng, Ashley Auerbach, Fang Li. Nature 2020
Jian Shang, Gang Ye, Ke Shi, Yushun Wan, Chuming Luo, Hideki Aihara, Qibin Geng, Ashley Auerbach, Fang Li. Nature 2020
3
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.