A citation-based method for searching scientific literature

Mauricio Esguerra, Alexey Siretskiy, Xabier Bello, Jessica Sallander, Hugo Gutiérrez-de-Terán. Nucleic Acids Res 2016
Times Cited: 48







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



Times Cited
  Times     Co-cited
Similarity


Trends in GPCR drug discovery: new agents, targets and indications.
Alexander S Hauser, Misty M Attwood, Mathias Rask-Andersen, Helgi B Schiöth, David E Gloriam. Nat Rev Drug Discov 2017
980
33

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
29

GOMoDo: A GPCRs online modeling and docking webserver.
Massimo Sandal, Tran Phuoc Duy, Matteo Cona, Hoang Zung, Paolo Carloni, Francesco Musiani, Alejandro Giorgetti. PLoS One 2013
54
27


Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.
Irina Kufareva, Vsevolod Katritch, Raymond C Stevens, Ruben Abagyan. Structure 2014
119
27

GPCRdb in 2018: adding GPCR structure models and ligands.
Gáspár Pándy-Szekeres, Christian Munk, Tsonko M Tsonkov, Stefan Mordalski, Kasper Harpsøe, Alexander S Hauser, Andrzej J Bojarski, David E Gloriam. Nucleic Acids Res 2018
269
25

The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints.
Robert Fredriksson, Malin C Lagerström, Lars-Gustav Lundin, Helgi B Schiöth. Mol Pharmacol 2003
20

Molecular signatures of G-protein-coupled receptors.
A J Venkatakrishnan, Xavier Deupi, Guillaume Lebon, Christopher G Tate, Gebhard F Schertler, M Madan Babu. Nature 2013
956
18

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
18

Crystal structure of rhodopsin: A G protein-coupled receptor.
K Palczewski, T Kumasaka, T Hori, C A Behnke, H Motoshima, B A Fox, I Le Trong, D C Teller, T Okada, R E Stenkamp,[...]. Science 2000
18

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.
Vadim Cherezov, Daniel M Rosenbaum, Michael A Hanson, Søren G F Rasmussen, Foon Sun Thian, Tong Sun Kobilka, Hee-Jung Choi, Peter Kuhn, William I Weis, Brian K Kobilka,[...]. Science 2007
18

GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors.
Catherine L Worth, Franziska Kreuchwig, Johanna K S Tiemann, Annika Kreuchwig, Michele Ritschel, Gunnar Kleinau, Peter W Hildebrand, Gerd Krause. Nucleic Acids Res 2017
18
50

Structural basis for allosteric regulation of GPCRs by sodium ions.
Wei Liu, Eugene Chun, Aaron A Thompson, Pavel Chubukov, Fei Xu, Vsevolod Katritch, Gye Won Han, Christopher B Roth, Laura H Heitman, Adriaan P IJzerman,[...]. Science 2012
661
16

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008.
Mayako Michino, Enrique Abola, Charles L Brooks, J Scott Dixon, John Moult, Raymond C Stevens. Nat Rev Drug Discov 2009
222
16

GPCR Dynamics: Structures in Motion.
Naomi R Latorraca, A J Venkatakrishnan, Ron O Dror. Chem Rev 2017
321
16

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
16

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment.
Irina Kufareva, Manuel Rueda, Vsevolod Katritch, Raymond C Stevens, Ruben Abagyan. Structure 2011
219
16

Pharmacogenomics of GPCR Drug Targets.
Alexander S Hauser, Sreenivas Chavali, Ikuo Masuho, Leonie J Jahn, Kirill A Martemyanov, David E Gloriam, M Madan Babu. Cell 2018
268
16

GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.
Catherine L Worth, Annika Kreuchwig, Gunnar Kleinau, Gerd Krause. BMC Bioinformatics 2011
44
15

Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors.
Lars Boukharta, Hugo Gutiérrez-de-Terán, Johan Aqvist. PLoS Comput Biol 2014
44
15




GPCRdb: an information system for G protein-coupled receptors.
Vignir Isberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S Hauser, Bas Vroling, Andrzej J Bojarski, Gert Vriend, David E Gloriam. Nucleic Acids Res 2016
162
12

A comprehensive map of molecular drug targets.
Rita Santos, Oleg Ursu, Anna Gaulton, A Patrícia Bento, Ramesh S Donadi, Cristian G Bologa, Anneli Karlsson, Bissan Al-Lazikani, Anne Hersey, Tudor I Oprea,[...]. Nat Rev Drug Discov 2017
879
12

Pathway and mechanism of drug binding to G-protein-coupled receptors.
Ron O Dror, Albert C Pan, Daniel H Arlow, David W Borhani, Paul Maragakis, Yibing Shan, Huafeng Xu, David E Shaw. Proc Natl Acad Sci U S A 2011
473
12

Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation.
Guillaume Lebon, Tony Warne, Patricia C Edwards, Kirstie Bennett, Christopher J Langmead, Andrew G W Leslie, Christopher G Tate. Nature 2011
613
12

Free energy calculations of A(2A) adenosine receptor mutation effects on agonist binding.
Henrik Keränen, Johan Åqvist, Hugo Gutiérrez-de-Terán. Chem Commun (Camb) 2015
25
24

Structural and energetic effects of A2A adenosine receptor mutations on agonist and antagonist binding.
Henrik Keränen, Hugo Gutiérrez-de-Terán, Johan Åqvist. PLoS One 2014
39
15

Characterization of the dynamic events of GPCRs by automated computational simulations.
Hugo Gutiérrez-de-Terán, Xabier Bello, David Rodríguez. Biochem Soc Trans 2013
33
18

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
Richard A Friesner, Jay L Banks, Robert B Murphy, Thomas A Halgren, Jasna J Klicic, Daniel T Mainz, Matthew P Repasky, Eric H Knoll, Mee Shelley, Jason K Perry,[...]. J Med Chem 2004
12

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
12

GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models.
Przemyslaw Miszta, Pawel Pasznik, Jakub Jakowiecki, Agnieszka Sztyler, Dorota Latek, Slawomir Filipek. Nucleic Acids Res 2018
20
30

Generic GPCR residue numbers - aligning topology maps while minding the gaps.
Vignir Isberg, Chris de Graaf, Andrea Bortolato, Vadim Cherezov, Vsevolod Katritch, Fiona H Marshall, Stefan Mordalski, Jean-Philippe Pin, Raymond C Stevens, Gerrit Vriend,[...]. Trends Pharmacol Sci 2015
236
10

Structure of the adenosine A(2A) receptor bound to an engineered G protein.
Byron Carpenter, Rony Nehmé, Tony Warne, Andrew G W Leslie, Christopher G Tate. Nature 2016
255
10

Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.
Alessandro Marchiori, Luciana Capece, Alejandro Giorgetti, Paolo Gasparini, Maik Behrens, Paolo Carloni, Wolfgang Meyerhof. PLoS One 2013
51
10

Coarse-grained model of proteins incorporating atomistic detail of the active site.
Marilisa Neri, Claudio Anselmi, Michele Cascella, Amos Maritan, Paolo Carloni. Phys Rev Lett 2005
109
10


Activation mechanism of the β2-adrenergic receptor.
Ron O Dror, Daniel H Arlow, Paul Maragakis, Thomas J Mildorf, Albert C Pan, Huafeng Xu, David W Borhani, David E Shaw. Proc Natl Acad Sci U S A 2011
367
10

Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison.
Dorota Latek, Pawel Pasznik, Teresa Carlomagno, Slawomir Filipek. PLoS One 2013
38
13


Structural modeling of G-protein coupled receptors: An overview on automatic web-servers.
Mirko Busato, Alejandro Giorgetti. Int J Biochem Cell Biol 2016
9
55

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.
G Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman. J Comput Aided Mol Des 2013
10

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.
Michael J Robertson, Julian Tirado-Rives, William L Jorgensen. J Chem Theory Comput 2015
308
10

Structural diversity of G protein-coupled receptors and significance for drug discovery.
Malin C Lagerström, Helgi B Schiöth. Nat Rev Drug Discov 2008
989
10

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
10

OPM database and PPM web server: resources for positioning of proteins in membranes.
Mikhail A Lomize, Irina D Pogozheva, Hyeon Joo, Henry I Mosberg, Andrei L Lomize. Nucleic Acids Res 2012
859
10

Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes.
Michael Leguèbe, Chuong Nguyen, Luciana Capece, Zung Hoang, Alejandro Giorgetti, Paolo Carloni. PLoS One 2012
34
14

Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis.
Fabrizio Fierro, Eda Suku, Mercedes Alfonso-Prieto, Alejandro Giorgetti, Sven Cichon, Paolo Carloni. Front Mol Biosci 2017
21
23

Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms.
Willem Jespers, Anke C Schiedel, Laura H Heitman, Robert M Cooke, Lisa Kleene, Gerard J P van Westen, David E Gloriam, Christa E Müller, Eddy Sotelo, Hugo Gutiérrez-de-Terán. Trends Pharmacol Sci 2018
35
14


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.