A citation-based method for searching scientific literature

Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson, Desmond G Higgins. Mol Syst Biol 2011
Times Cited: 8097







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



Times Cited
  Times     Co-cited
Similarity


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
14

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
14

Jalview Version 2--a multiple sequence alignment editor and analysis workbench.
Andrew M Waterhouse, James B Procter, David M A Martin, Michèle Clamp, Geoffrey J Barton. Bioinformatics 2009
12

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
9

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
8

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
8

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
7

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
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

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
7

Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
6

WebLogo: a sequence logo generator.
Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner. Genome Res 2004
6

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
6

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
6


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
5

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
5

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
5


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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
5


FastTree 2--approximately maximum-likelihood trees for large alignments.
Morgan N Price, Paramvir S Dehal, Adam P Arkin. PLoS One 2010
5


Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris Duran,[...]. Bioinformatics 2012
5

GROMACS: fast, flexible, and free.
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
4

Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
4

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
4

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
4

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
4

Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
4

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
4



AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
R A Laskowski, J A Rullmannn, M W MacArthur, R Kaptein, J M Thornton. J Biomol NMR 1996
4


The HADDOCK web server for data-driven biomolecular docking.
Sjoerd J de Vries, Marc van Dijk, Alexandre M J J Bonvin. Nat Protoc 2010
855
3

VERIFY3D: assessment of protein models with three-dimensional profiles.
D Eisenberg, R Lüthy, J U Bowie. Methods Enzymol 1997
3

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
3

A new coronavirus associated with human respiratory disease in China.
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
3

Toward the estimation of the absolute quality of individual protein structure models.
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
3

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
3

SignalP 4.0: discriminating signal peptides from transmembrane regions.
Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne, Henrik Nielsen. Nat Methods 2011
3

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel,[...]. Bioinformatics 2013
3

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.
Romelia Salomon-Ferrer, Andreas W Götz, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2013
3

Protein structure prediction and analysis using the Robetta server.
David E Kim, Dylan Chivian, David Baker. Nucleic Acids Res 2004
3

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
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.