Andrew M Waterhouse, James B Procter, David M A Martin, Michèle Clamp, Geoffrey J Barton. Bioinformatics 2009
Times Cited: 5046
Times Cited: 5046
Times Cited
Times Co-cited
Similarity
The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
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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
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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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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
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MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
Robert C Edgar. Nucleic Acids Res 2004
8
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
8
MolProbity: More and better reference data for improved all-atom structure validation.
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen,[...]. Protein Sci 2018
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen,[...]. Protein Sci 2018
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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
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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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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
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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
K J Livak, T D Schmittgen. Methods 2001
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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
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
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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
5
CDD/SPARCLE: the conserved domain database in 2020.
Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song,[...]. Nucleic Acids Res 2020
Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song,[...]. Nucleic Acids Res 2020
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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
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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Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
A Krogh, B Larsson, G von Heijne, E L Sonnhammer. J Mol Biol 2001
A Krogh, B Larsson, G von Heijne, E L Sonnhammer. J Mol Biol 2001
5
Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Ivica Letunic, Peer Bork. Nucleic Acids Res 2019
Ivica Letunic, Peer Bork. Nucleic Acids Res 2019
5
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
5
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
5
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
5
UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Elaine C Meng, Gregory S Couch, Tristan I Croll, John H Morris, Thomas E Ferrin. Protein Sci 2021
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Elaine C Meng, Gregory S Couch, Tristan I Croll, John H Morris, Thomas E Ferrin. Protein Sci 2021
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Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
4
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
4
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
4
Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
4
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
4
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
4
CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
4
The InterPro protein families and domains database: 20 years on.
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj,[...]. Nucleic Acids Res 2021
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj,[...]. Nucleic Acids Res 2021
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Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
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WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
4
ExPASy: The proteomics server for in-depth protein knowledge and analysis.
Elisabeth Gasteiger, Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D Appel, Amos Bairoch. Nucleic Acids Res 2003
Elisabeth Gasteiger, Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D Appel, Amos Bairoch. Nucleic Acids Res 2003
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The MEME Suite.
Timothy L Bailey, James Johnson, Charles E Grant, William S Noble. Nucleic Acids Res 2015
Timothy L Bailey, James Johnson, Charles E Grant, William S Noble. Nucleic Acids Res 2015
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Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.
Felix Gabler, Seung-Zin Nam, Sebastian Till, Milot Mirdita, Martin Steinegger, Johannes Söding, Andrei N Lupas, Vikram Alva. Curr Protoc Bioinformatics 2020
Felix Gabler, Seung-Zin Nam, Sebastian Till, Milot Mirdita, Martin Steinegger, Johannes Söding, Andrei N Lupas, Vikram Alva. Curr Protoc Bioinformatics 2020
3
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley Hintze, Li Wei Hung, Swati Jain, Airlie J McCoy,[...]. Acta Crystallogr D Struct Biol 2019
Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley Hintze, Li Wei Hung, Swati Jain, Airlie J McCoy,[...]. Acta Crystallogr D Struct Biol 2019
3
Overview of the CCP4 suite and current developments.
Martyn D Winn, Charles C Ballard, Kevin D Cowtan, Eleanor J Dodson, Paul Emsley, Phil R Evans, Ronan M Keegan, Eugene B Krissinel, Andrew G W Leslie, Airlie McCoy,[...]. Acta Crystallogr D Biol Crystallogr 2011
Martyn D Winn, Charles C Ballard, Kevin D Cowtan, Eleanor J Dodson, Paul Emsley, Phil R Evans, Ronan M Keegan, Eugene B Krissinel, Andrew G W Leslie, Airlie McCoy,[...]. Acta Crystallogr D Biol Crystallogr 2011
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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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JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.
Andreas Grote, Karsten Hiller, Maurice Scheer, Richard Münch, Bernd Nörtemann, Dietmar C Hempel, Dieter Jahn. Nucleic Acids Res 2005
Andreas Grote, Karsten Hiller, Maurice Scheer, Richard Münch, Bernd Nörtemann, Dietmar C Hempel, Dieter Jahn. Nucleic Acids Res 2005
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UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
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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
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Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
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STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
3
3
Ensembl 2020.
Andrew D Yates, Premanand Achuthan, Wasiu Akanni, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett,[...]. Nucleic Acids Res 2020
Andrew D Yates, Premanand Achuthan, Wasiu Akanni, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett,[...]. Nucleic Acids Res 2020
3
I-TASSER: a unified platform for automated protein structure and function prediction.
Ambrish Roy, Alper Kucukural, Yang Zhang. Nat Protoc 2010
Ambrish Roy, Alper Kucukural, Yang Zhang. Nat Protoc 2010
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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
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
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NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
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.