BibTeX¶
Below is a BibTeX file containing relevant literature.
@article{izadi2016accuracy,
title={Accuracy limit of rigid 3-point water models},
author={Izadi, Saeed and Onufriev, Alexey V},
journal={The Journal of chemical physics},
volume={145},
number={7},
year={2016},
publisher={AIP Publishing}
}
@article{tian2019ff19sb,
title={{ff19SB}: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution},
author={Tian, Chuan and Kasavajhala, Koushik and Belfon, Kellon AA and Raguette, Lauren and Huang, He and Migues, Angela N and Bickel, John and Wang, Yuzhang and Pincay, Jorge and Wu, Qin and others},
journal={Journal of chemical theory and computation},
volume={16},
number={1},
pages={528--552},
year={2019},
publisher={ACS Publications}
}
@article{michaud2011mdanalysis,
title={MDAnalysis: a toolkit for the analysis of molecular dynamics simulations},
author={Michaud-Agrawal, Naveen and Denning, Elizabeth J and Woolf, Thomas B and Beckstein, Oliver},
journal={Journal of computational chemistry},
volume={32},
number={10},
pages={2319--2327},
year={2011},
publisher={Wiley Online Library}
}
@ARTICLE{virtanen2020scipy,
author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
Haberland, Matt and Reddy, Tyler and Cournapeau, David and
Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
Kern, Robert and Larson, Eric and Carey, C J and
Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
{VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
Harris, Charles R. and Archibald, Anne M. and
Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and
{van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
title = {{{SciPy} 1.0: Fundamental Algorithms for Scientific
Computing in Python}},
journal = {Nature Methods},
year = {2020},
volume = {17},
pages = {261--272},
adsurl = {https://rdcu.be/b08Wh},
doi = {10.1038/s41592-019-0686-2},
}
@Article{ harris2020array,
title = {Array programming with {NumPy}},
author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
van der Walt and Ralf Gommers and Pauli Virtanen and David
Cournapeau and Eric Wieser and Julian Taylor and Sebastian
Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
Travis E. Oliphant},
year = {2020},
month = sep,
journal = {Nature},
volume = {585},
number = {7825},
pages = {357--362},
doi = {10.1038/s41586-020-2649-2},
publisher = {Springer Science and Business Media {LLC}},
url = {https://doi.org/10.1038/s41586-020-2649-2}
}
@article{berman2000protein,
title={The protein data bank},
author={Berman, Helen M and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, Talapady N and Weissig, Helge and Shindyalov, Ilya N and Bourne, Philip E},
journal={Nucleic acids research},
volume={28},
number={1},
pages={235--242},
year={2000},
publisher={Oxford University Press}
}
@article{nasu2021structure,
title={Structure-and mechanism-guided design of single fluorescent protein-based biosensors},
author={Nasu, Yusuke and Shen, Yi and Kramer, Luke and Campbell, Robert E},
journal={Nature chemical biology},
volume={17},
number={5},
pages={509--518},
year={2021},
publisher={Nature Publishing Group US New York}
}
@article{akiyama2012experimental,
title={Experimental identification and theoretical analysis of a thermally stabilized green fluorescent protein variant.},
author={Saori Akiyama and A. Suenaga and Takayuki Kobayashi and T. Kamioka and M. Taiji and Y. Kuroda},
journal={Biochemistry},
year={2012},
volume={51 40},
pages={ 7974-82 },
doi={10.1021/bi300580j}
}
@article{zimmer2002green,
title={Green fluorescent protein (GFP): applications, structure, and related photophysical behavior},
author={Zimmer, Marc},
journal={Chemical reviews},
volume={102},
number={3},
pages={759--782},
year={2002},
publisher={ACS Publications}
}
@article{kummer2000effects,
title={Effects of threonine 203 replacements on excited-state dynamics and fluorescence properties of the green fluorescent protein (GFP)},
author={Kummer, Andreas D and Wiehler, Jens and Rehaber, Hermann and Kompa, Christian and Steipe, Boris and Michel-Beyerle, Maria Elisabeth},
journal={The Journal of Physical Chemistry B},
volume={104},
number={19},
pages={4791--4798},
year={2000},
publisher={ACS Publications}
}
@article{shinobu2010visualizing,
title={Visualizing proton antenna in a high-resolution green fluorescent protein structure},
author={Shinobu, Ai and Palm, Gottfried J and Schierbeek, Abraham J and Agmon, Noam},
journal={Journal of the American Chemical Society},
volume={132},
number={32},
pages={11093--11102},
year={2010},
publisher={ACS Publications}
}
@article{jung2005photophysics,
title={The photophysics of green fluorescent protein: influence of the key amino acids at positions 65, 203, and 222},
author={Jung, Gregor and Wiehler, Jens and Zumbusch, Andreas},
journal={Biophysical journal},
volume={88},
number={3},
pages={1932--1947},
year={2005},
publisher={Elsevier}
}
@article{barondeau2002structural,
title={Structural chemistry of a green fluorescent protein Zn biosensor},
author={Barondeau, David P and Kassmann, Carey J and Tainer, John A and Getzoff, Elizabeth D},
journal={Journal of the American Chemical Society},
volume={124},
number={14},
pages={3522--3524},
year={2002},
publisher={ACS Publications}
}
@article{grigorenko2013first,
title={First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→ I→ B proton transfer route},
author={Grigorenko, Bella L and Nemukhin, Alexander V and Polyakov, Igor V and Morozov, Dmitry I and Krylov, Anna I},
journal={Journal of the American Chemical Society},
volume={135},
number={31},
pages={11541--11549},
year={2013},
publisher={ACS Publications}
}
@article{sengupta2021parameterization,
title={Parameterization of monovalent ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models},
author={Sengupta, Arkajyoti and Li, Zhen and Song, Lin Frank and Li, Pengfei and Merz Jr, Kenneth M},
journal={Journal of chemical information and modeling},
volume={61},
number={2},
pages={869--880},
year={2021},
publisher={ACS Publications}
}
@article{jurrus2018improvements,
title={Improvements to the APBS biomolecular solvation software suite},
author={Jurrus, Elizabeth and Engel, Dave and Star, Keith and Monson, Kyle and Brandi, Juan and Felberg, Lisa E and Brookes, David H and Wilson, Leighton and Chen, Jiahui and Liles, Karina and others},
journal={Protein Science},
volume={27},
number={1},
pages={112--128},
year={2018},
publisher={Wiley Online Library}
}
@article{liu2008geometrical,
title={Geometrical Preferences of the Hydrogen Bonds on Protein- Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations},
author={Liu, Zhiguo and Wang, Guitao and Li, Zhanting and Wang, Renxiao},
journal={Journal of Chemical Theory and Computation},
volume={4},
number={11},
pages={1959--1973},
year={2008},
publisher={ACS Publications}
}
@article{mcdonald1994satisfying,
title={Satisfying hydrogen bonding potential in proteins},
author={McDonald, Ian K and Thornton, Janet M},
journal={Journal of molecular biology},
volume={238},
number={5},
pages={777--793},
year={1994},
publisher={Elsevier}
}
@article{hubbard2010hydrogen,
title={Hydrogen bonds in proteins: role and strength},
author={Hubbard, Roderick E and Haider, M Kamran},
journal={Encyclopedia of life sciences},
volume={1},
pages={1--6},
year={2010},
publisher={John Wiley \& Sons, Ltd. Hoboken, NJ, USA}
}
@article{mantina2009consistent,
title={Consistent van der Waals radii for the whole main group},
author={Mantina, Manjeera and Chamberlin, Adam C and Valero, Rosendo and Cramer, Christopher J and Truhlar, Donald G},
journal={Journal of Physical Chemistry A},
volume={113},
number={19},
pages={5806--5812},
year={2009},
publisher={ACS Publications}
}
@article{prasher1992primary,
title={Primary structure of the Aequorea victoria green-fluorescent protein},
author={Prasher, Douglas C and Eckenrode, Virginia K and Ward, William W and Prendergast, Frank G and Cormier, Milton J},
journal={Gene},
volume={111},
number={2},
pages={229--233},
year={1992},
publisher={Elsevier}
}
@article{cormack1996facs,
title={FACS-optimized mutants of the green fluorescent protein (GFP)},
author={Cormack, Brendan P and Valdivia, Raphael H and Falkow, Stanley},
journal={Gene},
volume={173},
number={1},
pages={33--38},
year={1996},
publisher={Elsevier}
}
@inbook{cannon2008redox,
title={Redox-Sensitive Green Fluorescent Protein: Probes for Dynamic Intracellular Redox Responses. A Review},
ISBN={9781597451291},
issn={1940-6029},
url={http://dx.doi.org/10.1007/978-1-59745-129-1_4},
doi={10.1007/978-1-59745-129-1_4},
booktitle={Methods in Molecular Biology},
publisher={Humana Press},
author={Cannon, Mark B. and James Remington, S.},
year={2008},
pages={50-64}
}
@article{hanson2002green,
title={Green Fluorescent Protein Variants as Ratiometric Dual Emission pH Sensors. 1. Structural Characterization and Preliminary Application},
volume={41},
issn={1520-4995},
url={http://dx.doi.org/10.1021/bi026609p},
doi={10.1021/bi026609p},
number={52},
journal={Biochemistry},
publisher={American Chemical Society (ACS)},
author={Hanson, George T. and McAnaney, Tim B. and Park, Eun Sun and Rendell, Marla E. P. and Yarbrough, Daniel K. and Chu, Shaoyou and Xi, Lixuan and Boxer, Steven G. and Montrose, Marshall H. and Remington, S. James},
year={2002},
month=dec, pages={15477–15488}
}
@article{marques2003time,
title={Time-Dependent Density-Functional Approach for Biological Chromophores: The Case of the Green Fluorescent Protein},
volume={90},
issn={1079-7114},
url={http://dx.doi.org/10.1103/PhysRevLett.90.258101},
doi={10.1103/physrevlett.90.258101},
number={25},
journal={Physical Review Letters},
publisher={American Physical Society (APS)},
author={Marques, Miguel A. L. and López, Xabier and Varsano, Daniele and Castro, Alberto and Rubio, Angel},
year={2003},
month=jun
}
@article{park2016electric,
title={Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein},
volume={138},
issn={1520-5126},
url={http://dx.doi.org/10.1021/jacs.6b06833},
doi={10.1021/jacs.6b06833},
number={41},
journal={Journal of the American Chemical Society},
publisher={American Chemical Society (ACS)},
author={Park, Jae Woo and Rhee, Young Min},
year={2016},
month=oct, pages={13619–13629}
}
@article{song2010development,
title={Development of force field parameters for oxyluciferin on its electronic ground and excited states},
volume={111},
issn={1097-461X},
url={http://dx.doi.org/10.1002/qua.22957},
doi={10.1002/qua.22957},
number={15},
journal={International Journal of Quantum Chemistry},
publisher={Wiley},
author={Song, Chang‐Ik and Rhee, Young Min},
year={2010},
month=dec, pages={4091–4105}
}
@article{filippi2011bathochromic,
title={Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches},
volume={8},
issn={1549-9626},
url={http://dx.doi.org/10.1021/ct200704k},
doi={10.1021/ct200704k},
number={1},
journal={Journal of Chemical Theory and Computation},
publisher={American Chemical Society (ACS)},
author={Filippi, Claudia and Buda, Francesco and Guidoni, Leonardo and Sinicropi, Adalgisa},
year={2011},
month=dec, pages={112–124}
}
@article{bourne2024quantum,
title={Quantum dynamics of excited state proton transfer in green fluorescent protein},
volume={160},
issn={1089-7690},
url={http://dx.doi.org/10.1063/5.0188834},
doi={10.1063/5.0188834},
number={6},
journal={The Journal of Chemical Physics},
publisher={AIP Publishing},
author={Bourne-Worster, Susannah and Worth, Graham A.},
year={2024},
month=feb
}
@article{breyfogle2023molecular,
title={Molecular Dynamics Force Field Parameters for the EGFP Chromophore and Some of Its Analogues},
volume={127},
issn={1520-5207},
url={http://dx.doi.org/10.1021/acs.jpcb.3c01486},
doi={10.1021/acs.jpcb.3c01486},
number={26},
journal={The Journal of Physical Chemistry B},
publisher={American Chemical Society (ACS)},
author={Breyfogle, Kimberly L. and Blood, Dalton L. and Rosnik, Andreana M. and Krueger, Brent P.},
year={2023},
month=jun, pages={5772–5788}
}
@article{van2008balance,
title={Balance between Ultrafast Parallel Reactions in the Green Fluorescent Protein Has a Structural Origin},
volume={95},
issn={0006-3495},
url={http://dx.doi.org/10.1529/biophysj.108.129957},
doi={10.1529/biophysj.108.129957},
number={4},
journal={Biophysical Journal},
publisher={Elsevier BV},
author={van Thor, Jasper J. and Ronayne, Kate L. and Towrie, Michael and Sage, J. Timothy},
year={2008},
month=aug, pages={1902–1912}
}
@article{megley2008photophysics,
title={Photophysics and Dihedral Freedom of the Chromophore in Yellow, Blue, and Green Fluorescent Protein},
volume={113},
issn={1520-5207},
url={http://dx.doi.org/10.1021/jp806285s},
doi={10.1021/jp806285s},
number={1},
journal={The Journal of Physical Chemistry B},
publisher={American Chemical Society (ACS)},
author={Megley, Colleen M. and Dickson, Luisa A. and Maddalo, Scott L. and Chandler, Gabriel J. and Zimmer, Marc},
year={2008},
month=dec, pages={302–308}
}
@article{niwa1996chemical,
title={Chemical nature of the light emitter of the
Aequorea
green fluorescent protein},
volume={93},
issn={1091-6490},
url={http://dx.doi.org/10.1073/pnas.93.24.13617},
doi={10.1073/pnas.93.24.13617},
number={24},
journal={Proceedings of the National Academy of Sciences},
publisher={Proceedings of the National Academy of Sciences},
author={Niwa, Haruki and Inouye, Satoshi and Hirano, Takashi and Matsuno, Tatsuki and Kojima, Satoshi and Kubota, Masayuki and Ohashi, Mamoru and Tsuji, Frederick I.},
year={1996},
month=nov, pages={13617–13622}
}
@article{weber1999shedding,
title={Shedding light on the dark and weakly fluorescent states of green fluorescent proteins},
volume={96},
issn={1091-6490},
url={http://dx.doi.org/10.1073/pnas.96.11.6177},
doi={10.1073/pnas.96.11.6177},
number={11},
journal={Proceedings of the National Academy of Sciences},
publisher={Proceedings of the National Academy of Sciences},
author={Weber, Wolfgang and Helms, Volkhard and McCammon, J. Andrew and Langhoff, Peter W.},
year={1999},
month=may, pages={6177–6182}
}
@article{hanson2004investigating,
title={Investigating Mitochondrial Redox Potential with Redox-sensitive Green Fluorescent Protein Indicators},
volume={279},
issn={0021-9258},
url={http://dx.doi.org/10.1074/jbc.m312846200},
doi={10.1074/jbc.m312846200},
number={13},
journal={Journal of Biological Chemistry},
publisher={Elsevier BV},
author={Hanson, George T. and Aggeler, Robert and Oglesbee, Devin and Cannon, Mark and Capaldi, Roderick A. and Tsien, Roger Y. and Remington, S. James},
year={2004},
month=mar,
pages={13044-13053}
}
@article{remington2011green,
title={Green fluorescent protein: A perspective},
volume={20},
issn={1469-896X},
url={http://dx.doi.org/10.1002/pro.684},
doi={10.1002/pro.684},
number={9},
journal={Protein Science},
publisher={Wiley},
author={Remington, S. James},
year={2011},
month=jul,
pages={1509-1519}
}