A citation-based method for searching scientific literature

Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
Times Cited: 1214







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



Times Cited
  Times     Co-cited
Similarity


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
27

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
15

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
13

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
11

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
11






ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
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
8

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
8

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
7

VERIFY3D: assessment of protein models with three-dimensional profiles.
D Eisenberg, R Lüthy, J U Bowie. Methods Enzymol 1997
7

The Amber biomolecular simulation programs.
David A Case, Thomas E Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J Woods. J Comput Chem 2005
6

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
6

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
6


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
5


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
5

Toward the estimation of the absolute quality of individual protein structure models.
Pascal Benkert, Marco Biasini, Torsten Schwede. Bioinformatics 2011
5

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
438
5

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
5

The HHpred interactive server for protein homology detection and structure prediction.
Johannes Söding, Andreas Biegert, Andrei N Lupas. Nucleic Acids Res 2005
5



CHARMM-GUI: a web-based graphical user interface for CHARMM.
Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
5

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
4

Molecular Dynamics Simulation for All.
Scott A Hollingsworth, Ron O Dror. Neuron 2018
333
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

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
Paolo Di Tommaso, Sebastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, Cedric Notredame. Nucleic Acids Res 2011
641
4

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
4

JPred4: a protein secondary structure prediction server.
Alexey Drozdetskiy, Christian Cole, James Procter, Geoffrey J Barton. Nucleic Acids Res 2015
954
4

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
4


CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.
Emilia L Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C Song, Eder M Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M Venable,[...]. J Comput Chem 2014
956
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
4

CHARMM: the biomolecular simulation program.
B R Brooks, C L Brooks, A D Mackerell, L Nilsson, R J Petrella, B Roux, Y Won, G Archontis, C Bartels, S Boresch,[...]. J Comput Chem 2009
4

Scalable molecular dynamics with NAMD.
James C Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D Skeel, Laxmikant Kalé, Klaus Schulten. J Comput Chem 2005
4

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

Modeling of loops in protein structures.
A Fiser, R K Do, A Sali. Protein Sci 2000
3

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
3

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
3

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
3

PatchDock and SymmDock: servers for rigid and symmetric docking.
Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J Wolfson. Nucleic Acids Res 2005
3

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
3

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
A C Wallace, R A Laskowski, J M Thornton. Protein Eng 1995
3

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
Renhong Yan, Yuanyuan Zhang, Yaning Li, Lu Xia, Yingying Guo, Qiang Zhou. Science 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.