Structural Determinants of Improved Fluorescence ina Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins:Insights from Continuum Electrostatic Calculations and Molecular DynamicsSimulations

		BioNMR > Educational resources > Journal club
Structural Determinants of Improved Fluorescence ina Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins:Insights from Continuum Electrostatic Calculations and Molecular DynamicsSimulations

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

07-30-2016, 04:57 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Structural Determinants of Improved Fluorescence ina Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins:Insights from Continuum Electrostatic Calculations and Molecular DynamicsSimulations

Biochemistry
DOI: 10.1021/acs.biochem.6b00295

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Evaluation by fluorescence, STD-NMR, docking and semi-empirical calculations of the o-NBA photo-acid interaction with BSA. Evaluation by fluorescence, STD-NMR, docking and semi-empirical calculations of the o-NBA photo-acid interaction with BSA. Evaluation by fluorescence, STD-NMR, docking and semi-empirical calculations of the o-NBA photo-acid interaction with BSA. Spectrochim Acta A Mol Biomol Spectrosc. 2016 Jun 18;169:175-181 Authors: Chaves OA, Jesus CS, Cruz PF, Sant'Anna CM, Brito RM, Serpa C Abstract Serum albumins present reversible pH dependent conformational transitions. A sudden laser induced pH-jump is a methodology that can provide new...	nmrlearner	Journal club	0	07-06-2016 02:00 AM
Tolerance of a Knotted Near-Infrared Fluorescent Proteinto Random Circular Permutation Tolerance of a Knotted Near-Infrared Fluorescent Proteinto Random Circular Permutation http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00258/20160629/images/medium/bi-2016-00258j_0007.gif Biochemistry DOI: 10.1021/acs.biochem.6b00258 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/BFoPZHgtXaU More...	nmrlearner	Journal club	0	06-30-2016 02:26 AM
The CopC Family: Structural and Bioinformatic Insightsinto a Diverse Group of Periplasmic Copper Binding Proteins The CopC Family: Structural and Bioinformatic Insightsinto a Diverse Group of Periplasmic Copper Binding Proteins http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00175/20160406/images/medium/bi-2016-001758_0008.gif Biochemistry DOI: 10.1021/acs.biochem.6b00175 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/NhUil9uehKc More...	nmrlearner	Journal club	0	04-06-2016 10:29 PM
[NMR paper] Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations. Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations. Related Articles Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations. Phys Chem Chem Phys. 2015 Oct 9; Authors: Paluch P, Pawlak T, Jeziorna A, Trébosc J, Hou G, Vega AJ, Amoureux JP, Dracinsky M, Polenova T, Potrzebowski MJ Abstract We report a new multidimensional magic angle spinning...	nmrlearner	Journal club	0	10-10-2015 06:47 PM
Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings Abstract Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural...	nmrlearner	Journal club	0	06-26-2012 06:18 AM
[NMR paper] QSAR-by-NMR: quantitative insights into structural determinants for binding affinity QSAR-by-NMR: quantitative insights into structural determinants for binding affinity by analysis of 1H/15N chemical shift differences in MMP-3 ligands. Related Articles QSAR-by-NMR: quantitative insights into structural determinants for binding affinity by analysis of 1H/15N chemical shift differences in MMP-3 ligands. Bioorg Med Chem Lett. 2005 Apr 1;15(7):1779-83 Authors: Matter H, Schudok M, Elshorst B, Jacobs DM, Saxena K, Kogler H A novel strategy is applied to obtain quantitative insights on factors influencing biological affinity in...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides. Related Articles Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides. J Pept Res. 2003 Apr;61(4):177-88 Authors: Santiveri CM, Rico M, Jiménez MA, Pastor MT, Pérez-Payá E In a previous study we designed a 20-residue peptide able to adopt a significant population of a three-stranded...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. Related Articles Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J Biomol NMR. 1991 Nov;1(4):447-56 Authors: GÃ¼ntert P, WÃ¼thrich K A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...	nmrlearner	Journal club	0	08-21-2010 11:12 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off