The sequence–ensemble relationship in fuzzy protein complexes - pnas.org

		BioNMR > NMR community > Online News
The sequence–ensemble relationship in fuzzy protein complexes - pnas.org

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

09-10-2021, 01:39 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

The sequence–ensemble relationship in fuzzy protein complexes - pnas.org

The sequence–ensemble relationship in fuzzy protein complexes - pnas.org

The sequence–ensemble relationship in fuzzy protein complexes pnas.org Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
A cocrystal structure of dengue capsid protein in complex of inhibitor - pnas.org A cocrystal structure of dengue capsid protein in complex of inhibitor - pnas.org A cocrystal structure of dengue capsid protein in complex of inhibitor pnas.org Read here	nmrlearner	Online News	0	01-31-2021 02:47 PM
A cocrystal structure of dengue capsid protein in complex of inhibitor - pnas.org A cocrystal structure of dengue capsid protein in complex of inhibitor - pnas.org A cocrystal structure of dengue capsid protein in complex of inhibitor pnas.org Read here	nmrlearner	Online News	0	07-16-2020 09:01 PM
Relationship of Sequence and Phase Separation in ProteinLow-Complexity Regions Relationship of Sequence and Phase Separation in ProteinLow-Complexity Regions https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00008/20180316/images/medium/bi-2018-00008n_0006.gif Biochemistry DOI: 10.1021/acs.biochem.8b00008 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/8TxFxS7r55U More...	nmrlearner	Journal club	0	03-17-2018 12:12 PM
[NMR paper] The thermodynamic basis of the fuzzy interaction of an intrinsically disordered protein The thermodynamic basis of the fuzzy interaction of an intrinsically disordered protein Many intrinsically disordered proteins (IDP) that fold upon binding retain conformational heterogeneity in IDP-target complexes. The thermodynamics of such fuzzy interactions is poorly understood. Here we introduce a thermodynamic framework, based on analysis of ITC and CD spectroscopy data, that provides experimental description of IDP association in terms of folding and binding contributions which can be predicted using sequence folding propensities and molecular modeling. We show how IDP can...	nmrlearner	Journal club	0	09-15-2017 08:41 PM
[NMR paper] An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein-Peptide Complexes Characterized by NMR Spectroscopy. An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein-Peptide Complexes Characterized by NMR Spectroscopy. Related Articles An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein-Peptide Complexes Characterized by NMR Spectroscopy. Chembiochem. 2014 Feb 6; Authors: Guan JY, Foerster JM, Drijfhout JW, Timmer M, Blok A, Ullmann GM, Ubbink M Abstract Protein complex formation involves an encounter state in which the proteins are associated in a nonspecific manner and often stabilized by...	nmrlearner	Journal club	0	02-08-2014 05:45 PM
Fuzzy NMR Structures Get Sharper - The Biological SCENE http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcTewkunW2cElnFDlY_SHZKhJFhmDeBRbo9BesHt1yIlV8ubCY02W4b6PKIBRzy52Xj65SxFU3uT The Biological SCENE <img alt="" height="1" width="1" /> Fuzzy NMR Structures Get Sharper The Biological SCENE For protein structure determination, X-ray crystallography typically beats nuclear magnetic resonance (NMR) spectroscopy in terms of accuracy. But a computer program called Rosetta may help NMR catch up, chemists report. They used the program to refine ... Fuzzy NMR Structures Get Sharper - The Biological SCENE	nmrlearner	Online News	0	01-27-2014 09:59 PM
Sequence-Specific Mappingof the Interaction betweenUrea and Unfolded Ubiquitin from Ensemble Analysis of NMR and SmallAngle Scattering Data Sequence-Specific Mappingof the Interaction betweenUrea and Unfolded Ubiquitin from Ensemble Analysis of NMR and SmallAngle Scattering Data Jie-rong Huang, Frank Gabel, Malene Ringkjøbing Jensen, Stephan Grzesiek and Martin Blackledge http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2118688/aop/images/medium/ja-2011-118688_0007.gif Journal of the American Chemical Society DOI: 10.1021/ja2118688 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/u0K4iYUlStc	nmrlearner	Journal club	0	02-23-2012 07:38 AM
[NMR paper] Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and grap Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and graph theory. Related Articles Automation of protein 2D proton NMR assignment by means of fuzzy mathematics and graph theory. J Chem Inf Comput Sci. 1993 Sep-Oct;33(5):668-82 Authors: Xu J, Straus SK, Sanctuary BC, Trimble L The novel methodology for protein 2D NMR assignment presented in this paper is based upon protein spin coupling graph theory analysis, fuzzy graph pattern recognition, and tree searching. The method required to formalize the whole assignment...	nmrlearner	Journal club	0	08-22-2010 03:01 AM

« 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