Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances

		BioNMR > NMR community > Online News
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

03-24-2019, 10:41 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,188

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

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations Science AdvancesWe present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are ...

Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Blind protein structure prediction using accelerated free-energy simulations - Science Advances Blind protein structure prediction using accelerated free-energy simulations - Science Advances Blind protein structure prediction using accelerated free-energy simulations Science AdvancesWe report a key proof of principle of a new acceleration method for predicting protein structures by molecular ... Read here	nmrlearner	Online News	0	03-24-2019 10:41 PM
Blind protein structure prediction using accelerated free-energy simulations - Science Advances Blind protein structure prediction using accelerated free-energy simulations - Science Advances Blind protein structure prediction using accelerated free-energy simulations Science AdvancesWe report a key proof of principle of a new acceleration method for predicting protein structures by molecular ... Read here	nmrlearner	Online News	0	01-07-2019 05:49 AM
Molecular virologist fights influenza at the molecular level: A study of how experimental inhibitors bind a key flu protein may guide novel antiviral compounds - Science Daily Molecular virologist fights influenza at the molecular level: A study of how experimental inhibitors bind a key flu protein may guide novel antiviral compounds - Science Daily Molecular virologist fights influenza at the molecular level: A study of how experimental inhibitors bind a key flu protein may guide novel antiviral compounds Science DailyIn research to improve influenza therapies against H7N9 and other influenza strains, researchers have detailed the binding site and mechanism of inhibition for ... Read here	nmrlearner	Online News	0	01-07-2019 05:49 AM
Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00886/20171020/images/medium/bi-2017-008868_0004.gif Biochemistry DOI: 10.1021/acs.biochem.7b00886 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/vJJECwRnRgQ More...	nmrlearner	Journal club	0	10-24-2017 01:41 AM
[NMR paper] Molecular dynamics simulations on PGLa using NMR orientational constraints. Molecular dynamics simulations on PGLa using NMR orientational constraints. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Molecular dynamics simulations on PGLa using NMR orientational constraints. J Biomol NMR. 2015 Nov;63(3):265-74 Authors: Sternberg U, Witter R Abstract NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the...	nmrlearner	Journal club	0	08-25-2016 06:10 PM
[NMR paper] Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations. Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations. Related Articles Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations. J Chem Theory Comput. 2014 Apr 8;10(4):1781-7 Authors: Li DW, Brüschweiler R Abstract A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a...	nmrlearner	Journal club	0	11-22-2015 01:36 AM
Molecular dynamics simulations on PGLa using NMR orientational constraints Molecular dynamics simulations on PGLa using NMR orientational constraints Abstract NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics...	nmrlearner	Journal club	0	09-11-2015 06:48 AM
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...	nmrlearner	Journal club	0	02-11-2012 10:31 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