A citation-based method for searching scientific literature

Mariama Jaiteh, Ismael Rodríguez-Espigares, Jana Selent, Jens Carlsson. PLoS Comput Biol 2020
Times Cited: 20







List of co-cited articles
205 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
934
30

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
25

Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
25

Impact of GPCR Structures on Drug Discovery.
Miles Congreve, Chris de Graaf, Nigel A Swain, Christopher G Tate. Cell 2020
76
25

Ligand discovery from a dopamine D3 receptor homology model and crystal structure.
Jens Carlsson, Ryan G Coleman, Vincent Setola, John J Irwin, Hao Fan, Avner Schlessinger, Andrej Sali, Bryan L Roth, Brian K Shoichet. Nat Chem Biol 2011
222
25


Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment.
Jason S E Loo, Abigail L Emtage, Kar Weng Ng, Alene S J Yong, Stephen W Doughty. J Mol Graph Model 2018
12
33

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
20

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
259
20

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
20

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors.
Mauricio Esguerra, Alexey Siretskiy, Xabier Bello, Jessica Sallander, Hugo Gutiérrez-de-Terán. Nucleic Acids Res 2016
45
20

GPCRmd uncovers the dynamics of the 3D-GPCRome.
Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, Johanna K S Tiemann, David Aranda-García, Juan Manuel Ramírez-Anguita, Tomasz Maciej Stepniewski, Nathalie Worp, Alejandro Varela-Rial, Adrián Morales-Pastor, Brian Medel-Lacruz,[...]. Nat Methods 2020
32
20

Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist.
Ellen Y T Chien, Wei Liu, Qiang Zhao, Vsevolod Katritch, Gye Won Han, Michael A Hanson, Lei Shi, Amy Hauck Newman, Jonathan A Javitch, Vadim Cherezov,[...]. Science 2010
860
20

D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.
Sheng Wang, Daniel Wacker, Anat Levit, Tao Che, Robin M Betz, John D McCorvy, A J Venkatakrishnan, Xi-Ping Huang, Ron O Dror, Brian K Shoichet,[...]. Science 2017
107
20

How Ligands Illuminate GPCR Molecular Pharmacology.
Daniel Wacker, Raymond C Stevens, Bryan L Roth. Cell 2017
261
20

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
20

Molecular Dynamics Simulation for All.
Scott A Hollingsworth, Ron O Dror. Neuron 2018
306
20

Crystal structure of the β2 adrenergic receptor-Gs protein complex.
Søren G F Rasmussen, Brian T DeVree, Yaozhong Zou, Andrew C Kruse, Ka Young Chung, Tong Sun Kobilka, Foon Sun Thian, Pil Seok Chae, Els Pardon, Diane Calinski,[...]. Nature 2011
20

The Molecular Basis of G Protein-Coupled Receptor Activation.
William I Weis, Brian K Kobilka. Annu Rev Biochem 2018
338
20

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
20

Ultra-large library docking for discovering new chemotypes.
Jiankun Lyu, Sheng Wang, Trent E Balius, Isha Singh, Anat Levit, Yurii S Moroz, Matthew J O'Meara, Tao Che, Enkhjargal Algaa, Kateryna Tolmachova,[...]. Nature 2019
249
20

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
Michael M Mysinger, Michael Carchia, John J Irwin, Brian K Shoichet. J Med Chem 2012
852
20

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
20

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
15

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
15

Activation and allosteric modulation of a muscarinic acetylcholine receptor.
Andrew C Kruse, Aaron M Ring, Aashish Manglik, Jianxin Hu, Kelly Hu, Katrin Eitel, Harald Hübner, Els Pardon, Celine Valant, Patrick M Sexton,[...]. Nature 2013
589
15


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
15

An online resource for GPCR structure determination and analysis.
Christian Munk, Eshita Mutt, Vignir Isberg, Louise F Nikolajsen, Janne M Bibbe, Tilman Flock, Michael A Hanson, Raymond C Stevens, Xavier Deupi, David E Gloriam. Nat Methods 2019
70
15


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
849
15

Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site.
Pierre Matricon, Anirudh Ranganathan, Eugene Warnick, Zhan-Guo Gao, Axel Rudling, Catia Lambertucci, Gabriella Marucci, Aitakin Ezzati, Mariama Jaiteh, Diego Dal Ben,[...]. Sci Rep 2017
27
15

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.
Richard A Friesner, Robert B Murphy, Matthew P Repasky, Leah L Frye, Jeremy R Greenwood, Thomas A Halgren, Paul C Sanschagrin, Daniel T Mainz. J Med Chem 2006
15

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.
Yanyong Kang, X Edward Zhou, Xiang Gao, Yuanzheng He, Wei Liu, Andrii Ishchenko, Anton Barty, Thomas A White, Oleksandr Yefanov, Gye Won Han,[...]. Nature 2015
470
15

GPCR Dynamics: Structures in Motion.
Naomi R Latorraca, A J Venkatakrishnan, Ron O Dror. Chem Rev 2017
300
15

Structure-Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics.
Agnieszka A Kaczor, Andrea G Silva, María I Loza, Peter Kolb, Marián Castro, Antti Poso. ChemMedChem 2016
31
15

Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders.
P Jeffrey Conn, Arthur Christopoulos, Craig W Lindsley. Nat Rev Drug Discov 2009
759
15



Virtual fragment screening on GPCRs: a case study on dopamine D3 and histamine H4 receptors.
Márton Vass, Éva Schmidt, Ferenc Horti, György M Keserű. Eur J Med Chem 2014
35
15

A benchmarking study on virtual ligand screening against homology models of human GPCRs.
Victor Jun Yu Lim, Weina Du, Yu Zong Chen, Hao Fan. Proteins 2018
11
27

New Binding Sites, New Opportunities for GPCR Drug Discovery.
H C Stephen Chan, Yi Li, Thamani Dahoun, Horst Vogel, Shuguang Yuan. Trends Biochem Sci 2019
64
15

Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor.
Chris de Graaf, Albert J Kooistra, Henry F Vischer, Vsevolod Katritch, Martien Kuijer, Mitsunori Shiroishi, So Iwata, Tatsuro Shimamura, Raymond C Stevens, Iwan J P de Esch,[...]. J Med Chem 2011
146
15

Ligand pose and orientational sampling in molecular docking.
Ryan G Coleman, Michael Carchia, Teague Sterling, John J Irwin, Brian K Shoichet. PLoS One 2013
71
15

Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4.
Michael M Mysinger, Dahlia R Weiss, Joshua J Ziarek, Stéphanie Gravel, Allison K Doak, Joel Karpiak, Nikolaus Heveker, Brian K Shoichet, Brian F Volkman. Proc Natl Acad Sci U S A 2012
109
15

Docking Screens for Novel Ligands Conferring New Biology.
John J Irwin, Brian K Shoichet. J Med Chem 2016
140
15

A geometric approach to macromolecule-ligand interactions.
I D Kuntz, J M Blaney, S J Oatley, R Langridge, T E Ferrin. J Mol Biol 1982
15

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
15

Structure-Guided Screening for Functionally Selective D2 Dopamine Receptor Ligands from a Virtual Chemical Library.
Barbara Männel, Mariama Jaiteh, Alexey Zeifman, Alena Randakova, Dorothee Möller, Harald Hübner, Peter Gmeiner, Jens Carlsson. ACS Chem Biol 2017
26
15

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
15


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.