A citation-based method for searching scientific literature

Joel C D Kaufmann, Benjamin S Krause, Suliman Adam, Eglof Ritter, Igor Schapiro, Peter Hegemann, Franz J Bartl. Biophys J 2020
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity


Toward an understanding of the retinal chromophore in rhodopsin mimics.
Mark M Huntress, Samer Gozem, Konstantin R Malley, Askat E Jailaubekov, Chrysoula Vasileiou, Mikas Vengris, James H Geiger, Babak Borhan, Igor Schapiro, Delmar S Larsen,[...]. J Phys Chem B 2013
26
100

Jannaschia seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea.
Dong Han Choi, Hana Yi, Jongsik Chun, Byung Cheol Cho. Int J Syst Evol Microbiol 2006
21
100

Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology.
Federico Melaccio, María Del Carmen Marín, Alessio Valentini, Fabio Montisci, Silvia Rinaldi, Marco Cherubini, Xuchun Yang, Yoshitaka Kato, Michael Stenrup, Yoelvis Orozco-Gonzalez,[...]. J Chem Theory Comput 2016
33
100

Modern quantum chemistry with [Open]Molcas.
Francesco Aquilante, Jochen Autschbach, Alberto Baiardi, Stefano Battaglia, Veniamin A Borin, Liviu F Chibotaru, Irene Conti, Luca De Vico, Mickaël Delcey, Ignacio Fdez Galván,[...]. J Chem Phys 2020
52
100

Environment around the chromophore in pharaonis phoborhodopsin: mutation analysis of the retinal binding site.
K Shimono, Y Ikeura, Y Sudo, M Iwamoto, N Kamo. Biochim Biophys Acta 2001
61
100

ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation.
John Y Lin, Per Magne Knutsen, Arnaud Muller, David Kleinfeld, Roger Y Tsien. Nat Neurosci 2013
414
100

Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2.
Suliman Adam, Christian Wiebeler, Igor Schapiro. J Chem Theory Comput 2021
1
100

Red-shifting mutation of light-driven sodium-pump rhodopsin.
Keiichi Inoue, María Del Carmen Marín, Sahoko Tomida, Ryoko Nakamura, Yuta Nakajima, Massimo Olivucci, Hideki Kandori. Nat Commun 2019
24
100

A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties.
Yuki Sudo, Kunio Ihara, Shiori Kobayashi, Daisuke Suzuki, Hiroki Irieda, Takashi Kikukawa, Hideki Kandori, Michio Homma. J Biol Chem 2011
44
100

Improved prediction of protein side-chain conformations with SCWRL4.
Georgii G Krivov, Maxim V Shapovalov, Roland L Dunbrack. Proteins 2009
796
100

Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins.
Laura Pedraza-González, María Del Carmen Marín, Alejandro N Jorge, Tyler D Ruck, Xuchun Yang, Alessio Valentini, Massimo Olivucci, Luca De Vico. J Chem Inf Model 2020
7
100

Structure and mechanisms of sodium-pumping KR2 rhodopsin.
Kirill Kovalev, Vitaly Polovinkin, Ivan Gushchin, Alexey Alekseev, Vitaly Shevchenko, Valentin Borshchevskiy, Roman Astashkin, Taras Balandin, Dmitry Bratanov, Svetlana Vaganova,[...]. Sci Adv 2019
33
100

A color-determining amino acid residue of proteorhodopsin.
Yuya Ozaki, Takayoshi Kawashima, Rei Abe-Yoshizumi, Hideki Kandori. Biochemistry 2014
19
100

Diversification and spectral tuning in marine proteorhodopsins.
Dikla Man, Weiwu Wang, Gazalah Sabehi, L Aravind, Anton F Post, Ramon Massana, Elena N Spudich, John L Spudich, Oded Béjà. EMBO J 2003
200
100

Electrostatic Spectral Tuning Maps for Biological Chromophores.
Yoelvis Orozco-Gonzalez, Mohammad Pabel Kabir, Samer Gozem. J Phys Chem B 2019
13
100

A blue-shifted light-driven proton pump for neural silencing.
Yuki Sudo, Ayako Okazaki, Hikaru Ono, Jin Yagasaki, Seiya Sugo, Motoshi Kamiya, Louisa Reissig, Keiichi Inoue, Kunio Ihara, Hideki Kandori,[...]. J Biol Chem 2013
46
100

Femtosecond-to-millisecond structural changes in a light-driven sodium pump.
Petr Skopintsev, David Ehrenberg, Tobias Weinert, Daniel James, Rajiv K Kar, Philip J M Johnson, Dmitry Ozerov, Antonia Furrer, Isabelle Martiel, Florian Dworkowski,[...]. Nature 2020
26
100

Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
100

NeoR, a near-infrared absorbing rhodopsin.
Matthias Broser, Anika Spreen, Patrick E Konold, Enrico Peter, Suliman Adam, Veniamin Borin, Igor Schapiro, Reinhard Seifert, John T M Kennis, Yinth Andrea Bernal Sierra,[...]. Nat Commun 2020
8
100

Evolution of dim-light and color vision pigments.
Shozo Yokoyama. Annu Rev Genomics Hum Genet 2008
147
100

Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment.
Joseph P Bielawski, Katherine A Dunn, Gazalah Sabehi, Oded Béjà. Proc Natl Acad Sci U S A 2004
48
100

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.
Oliver P Ernst, David T Lodowski, Marcus Elstner, Peter Hegemann, Leonid S Brown, Hideki Kandori. Chem Rev 2014
523
100

Relocating the active-site lysine in rhodopsin and implications for evolution of retinylidene proteins.
Erin L Devine, Daniel D Oprian, Douglas L Theobald. Proc Natl Acad Sci U S A 2013
21
100

a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement.
Laura Pedraza-González, Luca De Vico, Marı A Del Carmen Marı N, Francesca Fanelli, Massimo Olivucci. J Chem Theory Comput 2019
17
100

Molecular and evolutionary aspects of microbial sensory rhodopsins.
Keiichi Inoue, Takashi Tsukamoto, Yuki Sudo. Biochim Biophys Acta 2014
43
100


Structural basis of the green-blue color switching in proteorhodopsin as determined by NMR spectroscopy.
Jiafei Mao, Nhu-Nguyen Do, Frank Scholz, Lenica Reggie, Michaela Mehler, Andrea Lakatos, Yean-Sin Ong, Sandra J Ullrich, Lynda J Brown, Richard C D Brown,[...]. J Am Chem Soc 2014
32
100

Frontiers in Multiscale Modeling of Photoreceptor Proteins.
Maria-Andrea Mroginski, Suliman Adam, Gil S Amoyal, Avishai Barnoy, Ana-Nicoleta Bondar, Veniamin A Borin, Jonathan R Church, Tatiana Domratcheva, Bernd Ensing, Francesca Fanelli,[...]. Photochem Photobiol 2021
3
100

Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins.
Kazuhiro Fujimoto, Shigehiko Hayashi, Jun-Ya Hasegawa, Hiroshi Nakatsuji. J Chem Theory Comput 2007
85
100

Multistate Multiconfiguration Quantum Chemical Computation of the Two-Photon Absorption Spectra of Bovine Rhodopsin.
Samira Gholami, Laura Pedraza-González, Xuchun Yang, Alexander A Granovsky, Ilya N Ioffe, Massimo Olivucci. J Phys Chem Lett 2019
5
100

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores.
Samer Gozem, Hoi Ling Luk, Igor Schapiro, Massimo Olivucci. Chem Rev 2017
107
100

A light-driven sodium ion pump in marine bacteria.
Keiichi Inoue, Hikaru Ono, Rei Abe-Yoshizumi, Susumu Yoshizawa, Hiroyasu Ito, Kazuhiro Kogure, Hideki Kandori. Nat Commun 2013
211
100

Crystal structure of the red light-activated channelrhodopsin Chrimson.
Kazumasa Oda, Johannes Vierock, Satomi Oishi, Silvia Rodriguez-Rozada, Reiya Taniguchi, Keitaro Yamashita, J Simon Wiegert, Tomohiro Nishizawa, Peter Hegemann, Osamu Nureki. Nat Commun 2018
41
100


Directed evolution of Gloeobacter violaceus rhodopsin spectral properties.
Martin K M Engqvist, R Scott McIsaac, Peter Dollinger, Nicholas C Flytzanis, Michael Abrams, Stanford Schor, Frances H Arnold. J Mol Biol 2015
43
100

A natural light-driven inward proton pump.
Keiichi Inoue, Shota Ito, Yoshitaka Kato, Yurika Nomura, Mikihiro Shibata, Takayuki Uchihashi, Satoshi P Tsunoda, Hideki Kandori. Nat Commun 2016
61
100

Atomistic design of microbial opsin-based blue-shifted optogenetics tools.
Hideaki E Kato, Motoshi Kamiya, Seiya Sugo, Jumpei Ito, Reiya Taniguchi, Ayaka Orito, Kunio Hirata, Ayumu Inutsuka, Akihiro Yamanaka, Andrés D Maturana,[...]. Nat Commun 2015
46
100

Quantum chemical modeling of rhodopsin mutants displaying switchable colors.
Federico Melaccio, Nicolas Ferré, Massimo Olivucci. Phys Chem Chem Phys 2012
43
100

Proteorhodopsin phototrophy in the ocean.
O Béjà, E N Spudich, J L Spudich, M Leclerc, E F DeLong. Nature 2001
469
100


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.