705 related articles for article (PubMed ID: 20977248)
1. Quantum refinement of protein structures: implementation and application to the red fluorescent protein DsRed.M1.
Hsiao YW; Sanchez-Garcia E; Doerr M; Thiel W
J Phys Chem B; 2010 Nov; 114(46):15413-23. PubMed ID: 20977248
[TBL] [Abstract][Full Text] [Related]
2. QM/MM study of the monomeric red fluorescent protein DsRed.M1.
Sanchez-Garcia E; Doerr M; Hsiao YW; Thiel W
J Phys Chem B; 2009 Dec; 113(52):16622-31. PubMed ID: 19994834
[TBL] [Abstract][Full Text] [Related]
3. QM/MM study of the absorption spectra of DsRed.M1 chromophores.
Sanchez-Garcia E; Doerr M; Thiel W
J Comput Chem; 2010 Jun; 31(8):1603-12. PubMed ID: 20014299
[TBL] [Abstract][Full Text] [Related]
4. QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed.
Sun Q; Doerr M; Li Z; Smith SC; Thiel W
Phys Chem Chem Phys; 2010 Mar; 12(10):2450-8. PubMed ID: 20449359
[TBL] [Abstract][Full Text] [Related]
5. pB(2) intermediate of the photoactive yellow protein: structure and excitation energies.
Hsiao YW; Thiel W
J Phys Chem B; 2011 Mar; 115(9):2097-106. PubMed ID: 21319777
[TBL] [Abstract][Full Text] [Related]
6. Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation.
Tubbs JL; Tainer JA; Getzoff ED
Biochemistry; 2005 Jul; 44(29):9833-40. PubMed ID: 16026155
[TBL] [Abstract][Full Text] [Related]
7. Excited states of fluorescent proteins, mKO and DsRed: chromophore-protein electrostatic interaction behind the color variations.
Hasegawa JY; Ise T; Fujimoto KJ; Kikuchi A; Fukumura E; Miyawaki A; Shiro Y
J Phys Chem B; 2010 Mar; 114(8):2971-9. PubMed ID: 20131896
[TBL] [Abstract][Full Text] [Related]
8. Red fluorescent protein DsRed: parametrization of its chromophore as an amino acid residue for computer modeling in the OPLS-AA force field.
Dmitrienko DV; Vrzheshch EP; Drutsa VL; Vrzheshch PV
Biochemistry (Mosc); 2006 Oct; 71(10):1133-52. PubMed ID: 17125463
[TBL] [Abstract][Full Text] [Related]
9. Molecular modeling of green fluorescent protein: structural effects of chromophore deprotonation.
Patnaik SS; Trohalaki S; Pachter R
Biopolymers; 2004 Dec; 75(6):441-52. PubMed ID: 15497152
[TBL] [Abstract][Full Text] [Related]
10. Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations.
Cauët E; Bogatko S; Weare JH; Fulton JL; Schenter GK; Bylaska EJ
J Chem Phys; 2010 May; 132(19):194502. PubMed ID: 20499974
[TBL] [Abstract][Full Text] [Related]
11. Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits).
Taguchi N; Mochizuki Y; Nakano T; Amari S; Fukuzawa K; Ishikawa T; Sakurai M; Tanaka S
J Phys Chem B; 2009 Jan; 113(4):1153-61. PubMed ID: 19127982
[TBL] [Abstract][Full Text] [Related]
12. QM/MM calculation of solvent effects on absorption spectra of guanine.
Parac M; Doerr M; Marian CM; Thiel W
J Comput Chem; 2010 Jan; 31(1):90-106. PubMed ID: 19412906
[TBL] [Abstract][Full Text] [Related]
13. Understanding rhodopsin mutations linked to the retinitis pigmentosa disease: a QM/MM and DFT/MRCI study.
Hernández-Rodríguez EW; Sánchez-García E; Crespo-Otero R; Montero-Alejo AL; Montero LA; Thiel W
J Phys Chem B; 2012 Jan; 116(3):1060-76. PubMed ID: 22126625
[TBL] [Abstract][Full Text] [Related]
14. Modeling photoabsorption of the asFP595 chromophore.
Bravaya KB; Bochenkova AV; Granovsky AA; Savitsky AP; Nemukhin AV
J Phys Chem A; 2008 Sep; 112(37):8804-10. PubMed ID: 18729441
[TBL] [Abstract][Full Text] [Related]
15. Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595.
Grigorenko B; Savitsky A; Topol I; Burt S; Nemukhin A
J Phys Chem B; 2006 Sep; 110(37):18635-40. PubMed ID: 16970493
[TBL] [Abstract][Full Text] [Related]
16. Computational strategy for tuning spectral properties of red fluorescent proteins.
Topol I; Collins J; Savitsky A; Nemukhin A
Biophys Chem; 2011 Oct; 158(2-3):91-5. PubMed ID: 21652139
[TBL] [Abstract][Full Text] [Related]
17. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
Riccardi D; Schaefer P; Cui Q
J Phys Chem B; 2005 Sep; 109(37):17715-33. PubMed ID: 16853267
[TBL] [Abstract][Full Text] [Related]
18. Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611.
Nienhaus K; Nar H; Heilker R; Wiedenmann J; Nienhaus GU
J Am Chem Soc; 2008 Sep; 130(38):12578-9. PubMed ID: 18761441
[TBL] [Abstract][Full Text] [Related]
19. Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.
Yu N; Yennawar HP; Merz KM
Acta Crystallogr D Biol Crystallogr; 2005 Mar; 61(Pt 3):322-32. PubMed ID: 15735343
[TBL] [Abstract][Full Text] [Related]
20. Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations.
Xiong Y; Lu HT; Zhan CG
J Comput Chem; 2008 Jun; 29(8):1259-67. PubMed ID: 18161687
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
