A citation-based method for searching scientific literature

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







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



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
20

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
18

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
17

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp, Torsten Schwede. Bioinformatics 2006
15



MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
7

QMEAN: A comprehensive scoring function for model quality assessment.
Pascal Benkert, Silvio C E Tosatto, Dietmar Schomburg. Proteins 2008
637
7

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
7

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
7

SWISS-MODEL: An automated protein homology-modeling server.
Torsten Schwede, Jürgen Kopp, Nicolas Guex, Manuel C Peitsch. Nucleic Acids Res 2003
6

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
6

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
6


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
6

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
5

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
5

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
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
5

QMEANDisCo-distance constraints applied on model quality estimation.
Gabriel Studer, Christine Rempfer, Andrew M Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede. Bioinformatics 2020
152
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
5

Features and development of Coot.
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
323
4


QMEAN server for protein model quality estimation.
Pascal Benkert, Michael Künzli, Torsten Schwede. Nucleic Acids Res 2009
493
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
304
4

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
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
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
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
4


MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, Sudhir Kumar. Mol Biol Evol 2013
4





cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
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
4

Advances in homology protein structure modeling.
Zhexin Xiang. Curr Protein Pept Sci 2006
242
4

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
4

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
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
431
3

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
3

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
158
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
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
885
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
3

3Drefine: an interactive web server for efficient protein structure refinement.
Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng. Nucleic Acids Res 2016
181
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
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.