BPG is committed to discovery and dissemination of knowledge
Cited by in F6Publishing
For: Pedraza-González L, De Vico L, Marı N MADC, Fanelli F, Olivucci M. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. J Chem Theory Comput 2019;15:3134-52. [PMID: 30916955 DOI: 10.1021/acs.jctc.9b00061] [Cited by in Crossref: 19] [Cited by in F6Publishing: 20] [Article Influence: 6.3] [Reference Citation Analysis]
Number Citing Articles
1 Tsujimura M, Tamura H, Saito K, Ishikita H. Absorption wavelength along chromophore low-barrier hydrogen bonds. iScience 2022;25:104247. [DOI: 10.1016/j.isci.2022.104247] [Cited by in Crossref: 2] [Article Influence: 2.0] [Reference Citation Analysis]
2 Pedraza-González L, Barneschi L, Padula D, De Vico L, Olivucci M. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol. Top Curr Chem (Cham) 2022;380:21. [PMID: 35291019 DOI: 10.1007/s41061-022-00374-w] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
3 Kim TI, Ha JK, Min SK. Coupled- and Independent-Trajectory Approaches Based on the Exact Factorization Using the PyUNIxMD Package. Top Curr Chem (Cham) 2022;380:8. [PMID: 35083549 DOI: 10.1007/s41061-021-00361-7] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
4 Nakajima Y, Pedraza-González L, Barneschi L, Inoue K, Olivucci M, Kandori H. Pro219 is an electrostatic color determinant in the light-driven sodium pump KR2. Commun Biol 2021;4:1185. [PMID: 34645937 DOI: 10.1038/s42003-021-02684-z] [Cited by in F6Publishing: 3] [Reference Citation Analysis]
5 Dratch BD, Orozco-Gonzalez Y, Gadda G, Gozem S. Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider Solution Ions. J Phys Chem Lett 2021;12:8384-96. [PMID: 34435784 DOI: 10.1021/acs.jpclett.1c02173] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
6 Nikolaev DM, Manathunga M, Orozco-Gonzalez Y, Shtyrov AA, Guerrero Martínez YO, Gozem S, Ryazantsev MN, Coutinho K, Canuto S, Olivucci M. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. J Chem Theory Comput 2021. [PMID: 34379429 DOI: 10.1021/acs.jctc.1c00221] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
7 Adam S, Wiebeler C, Schapiro I. Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2. J Chem Theory Comput 2021. [PMID: 34255519 DOI: 10.1021/acs.jctc.1c00160] [Cited by in F6Publishing: 5] [Reference Citation Analysis]
8 Lee IS, Ha JK, Han D, Kim TI, Moon SW, Min SK. PyUNIxMD: A Python-based excited state molecular dynamics package. J Comput Chem 2021;42:1755-66. [PMID: 34197646 DOI: 10.1002/jcc.26711] [Cited by in Crossref: 1] [Cited by in F6Publishing: 7] [Article Influence: 1.0] [Reference Citation Analysis]
9 Inoue K, Karasuyama M, Nakamura R, Konno M, Yamada D, Mannen K, Nagata T, Inatsu Y, Yawo H, Yura K, Béjà O, Kandori H, Takeuchi I. Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design. Commun Biol 2021;4:362. [PMID: 33742139 DOI: 10.1038/s42003-021-01878-9] [Cited by in Crossref: 1] [Cited by in F6Publishing: 4] [Article Influence: 1.0] [Reference Citation Analysis]
10 Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021;97:243-69. [PMID: 33369749 DOI: 10.1111/php.13372] [Cited by in Crossref: 2] [Cited by in F6Publishing: 7] [Article Influence: 2.0] [Reference Citation Analysis]
11 Tsujimura M, Ishikita H. Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins. J Phys Chem B 2020;124:11819-26. [PMID: 33236904 DOI: 10.1021/acs.jpcb.0c08910] [Cited by in Crossref: 6] [Cited by in F6Publishing: 10] [Article Influence: 3.0] [Reference Citation Analysis]
12 Nikolaev DM, Shtyrov AA, Mereshchenko AS, Panov MS, Tveryanovich YS, Ryazantsev MN. An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins' first spectral absorption band maxima. Phys Chem Chem Phys 2020;22:18114-23. [PMID: 32761024 DOI: 10.1039/d0cp02638g] [Cited by in Crossref: 5] [Cited by in F6Publishing: 6] [Article Influence: 2.5] [Reference Citation Analysis]
13 Mai S, González L. Molekulare Photochemie: Moderne Entwicklungen in der theoretischen Chemie. Angew Chem 2020;132:16976-92. [DOI: 10.1002/ange.201916381] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
14 Mai S, González L. Molecular Photochemistry: Recent Developments in Theory. Angew Chem Int Ed Engl 2020;59:16832-46. [PMID: 32052547 DOI: 10.1002/anie.201916381] [Cited by in Crossref: 34] [Cited by in F6Publishing: 49] [Article Influence: 17.0] [Reference Citation Analysis]
15 Aquilante F, Autschbach J, Baiardi A, Battaglia S, Borin VA, Chibotaru LF, Conti I, De Vico L, Delcey M, Fdez Galván I, Ferré N, Freitag L, Garavelli M, Gong X, Knecht S, Larsson ED, Lindh R, Lundberg M, Malmqvist PÅ, Nenov A, Norell J, Odelius M, Olivucci M, Pedersen TB, Pedraza-González L, Phung QM, Pierloot K, Reiher M, Schapiro I, Segarra-Martí J, Segatta F, Seijo L, Sen S, Sergentu DC, Stein CJ, Ungur L, Vacher M, Valentini A, Veryazov V. Modern quantum chemistry with [Open]Molcas. J Chem Phys 2020;152:214117. [PMID: 32505150 DOI: 10.1063/5.0004835] [Cited by in F6Publishing: 114] [Reference Citation Analysis]
16 Nakliang P, Lazim R, Chang H, Choi S. Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies. Biomolecules 2020;10:E631. [PMID: 32325877 DOI: 10.3390/biom10040631] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
17 Pedraza-González L, Marín MDC, Jorge AN, Ruck TD, Yang X, Valentini A, Olivucci M, De Vico L. Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins. J Chem Inf Model 2020;60:1481-93. [PMID: 31909998 DOI: 10.1021/acs.jcim.9b00615] [Cited by in Crossref: 6] [Cited by in F6Publishing: 9] [Article Influence: 3.0] [Reference Citation Analysis]
18 Groenhof G, Modi V, Morozov D. Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations. Curr Opin Struct Biol 2020;61:106-12. [PMID: 31927414 DOI: 10.1016/j.sbi.2019.12.013] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
19 Gholami S, Pedraza-González L, Yang X, Granovsky AA, Ioffe IN, Olivucci M. Multistate Multiconfiguration Quantum Chemical Computation of the Two-Photon Absorption Spectra of Bovine Rhodopsin. J Phys Chem Lett 2019;10:6293-300. [PMID: 31545053 DOI: 10.1021/acs.jpclett.9b02291] [Cited by in Crossref: 4] [Cited by in F6Publishing: 6] [Article Influence: 1.3] [Reference Citation Analysis]
20 Pieri E, Ledentu V, Sahlin M, Dehez F, Olivucci M, Ferré N. CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum. J Chem Theory Comput 2019;15:4535-46. [PMID: 31264415 DOI: 10.1021/acs.jctc.9b00221] [Cited by in Crossref: 8] [Cited by in F6Publishing: 8] [Article Influence: 2.7] [Reference Citation Analysis]