NMR paper Structure–Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System**

		BioNMR > Educational resources > Journal club
[NMR paper] Structure–Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System**

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

03-20-2021, 02:31 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

Structure–Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System**

Structure–Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System**

Angewandte Chemie International Edition, EarlyView.

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Model learns how individual amino acids determine protein function - The MIT Tech Model learns how individual amino acids determine protein function - The MIT Tech Model learns how individual amino acids determine protein function The MIT TechA machine-learning model from MIT researchers computationally breaks down how segments of amino acid chains determine a protein's function, which could ... Read here	nmrlearner	Online News	0	04-22-2019 06:11 PM
[NMR paper] REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment. REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment. REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment. ACS Cent Sci. 2018 Jan 24;4(1):89-96 Authors: Yang H, Staveness D, Ryckbosch SM, Axtman AD, Loy BA, Barnes AB, Pande VS, Schaefer J, Wender PA, Cegelski L Abstract Bryostatin 1 (henceforth bryostatin) is in clinical trials for the treatment of Alzheimer's disease and for HIV/AIDS eradication. It is also a preclinical lead for cancer...	nmrlearner	Journal club	0	02-03-2018 02:16 PM
[NMR paper] NMR Insight into Myosin-Binding Subunit Coiled Coil Structure Reveals Binding Interface with Protein Kinase G-I? Leucine Zipper in Vascular Function. NMR Insight into Myosin-Binding Subunit Coiled Coil Structure Reveals Binding Interface with Protein Kinase G-I? Leucine Zipper in Vascular Function. Related Articles NMR Insight into Myosin-Binding Subunit Coiled Coil Structure Reveals Binding Interface with Protein Kinase G-I? Leucine Zipper in Vascular Function. J Biol Chem. 2017 Mar 09;: Authors: Sharma AK, Birrane GG, Anklin C, Rigby AC, Alper SL Abstract Nitrovasodilators relax vascular smooth muscle cells (VSMC) in part by modulating the interaction of the C-terminal...	nmrlearner	Journal club	0	03-11-2017 05:12 PM
Synergistic Biomineralization Phenomena Created bya Combinatorial Nacre Protein Model System Synergistic Biomineralization Phenomena Created bya Combinatorial Nacre Protein Model System http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00163/20160412/images/medium/bi-2016-00163m_0008.gif Biochemistry DOI: 10.1021/acs.biochem.6b00163 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/ymKh5Kh3glo More...	nmrlearner	Journal club	0	04-13-2016 10:23 PM
Study reveals molecular function of protein essential for replication of H5N1 ... - News-Medical.net Study reveals molecular function of protein essential for replication of H5N1 ... - News-Medical.net http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcQqQVkN2sOlkhvYowf7yXaO0RlhCYQZ_9zOSx7m7tG2kLZe9aCik1IvkvJcZVU-_BYhJS__lMZX News-Medical.net <img alt="" height="1" width="1"> Study reveals molecular function of protein essential for replication of H5N1 ... News-Medical.net An international collaboration of scientists from the CEA, CNRS, University Joseph Fourier, the EMBL and the ILL has revealed the molecular function of a protein essential for replication of H5N1 influenza...	nmrlearner	Online News	0	12-10-2015 05:49 PM
Study of PEGylated model protein reveals porous structure based on PEG size - Phys.Org Study of PEGylated model protein reveals porous structure based on PEG size - Phys.Org http://www.bionmr.com//t2.gstatic.com/images?q=tbn:ANd9GcQdT1VtDs_349GghNDjMV50tdw7g0UzZNnkRkMt-SgVH2a6hHSvjT8JY4N42n5PGHBQ_JntWNc Phys.Org <img alt="" height="1" width="1"> Study of PEGylated model protein reveals porous structure based on PEG size Phys.Org NMR studies using 1H-15N heteronuclear single-quantum correlation spectroscopy showed that the PEG-Pc had well-dispersed resonances that indicated the protein remained folded in a stable conformation. Chemical shift perturbations were only...	nmrlearner	Online News	0	09-22-2015 06:40 PM
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function. Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function. Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function. Proteins. 2011 Oct;79(10):2988-91 Authors: Aramini JM, Rossi P, Fischer M, Xiao R, Acton TB, Montelione GT Abstract Protein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80-residue VF0530 protein from Vibrio fischeri,...	nmrlearner	Journal club	0	09-10-2011 06:51 PM
[NMR paper] The effects of proteins on [Ca2+] measurement: different effects on fluorescent and N The effects of proteins on measurement: different effects on fluorescent and NMR methods. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The effects of proteins on measurement: different effects on fluorescent and NMR methods. Cell Calcium. 1996 Nov;20(5):425-30 Authors: Matsuda S, Kusuoka H, Hashimoto K, Tsujimura E, Nishimura T Previous reports showed that the presence of proteins shifts the apparent dissociation constant (Kd) of a fluorescent dye indicator to...	nmrlearner	Journal club	0	08-22-2010 02:20 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