Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics - pnas.org

		BioNMR > NMR community > Online News
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics - 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

11-09-2024, 06:03 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,731

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

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics - pnas.org

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics - pnas.org

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics pnas.org Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Threading single proteins through pores to compare their energy landscapes \| Proceedings of the National Academy of Sciences - pnas.org Threading single proteins through pores to compare their energy landscapes \| Proceedings of the National Academy of Sciences - pnas.org Threading single proteins through pores to compare their energy landscapes \| Proceedings of the National Academy of Sciences pnas.org Read here	nmrlearner	Online News	0	10-06-2022 06:14 PM
[NMR paper] NMR Methods to Dissect the Molecular Mechanisms of Disease-Related Mutations (DRMs): Understanding How DRMs Remodel Functional Free Energy Landscapes. NMR Methods to Dissect the Molecular Mechanisms of Disease-Related Mutations (DRMs): Understanding How DRMs Remodel Functional Free Energy Landscapes. Related Articles NMR Methods to Dissect the Molecular Mechanisms of Disease-Related Mutations (DRMs): Understanding How DRMs Remodel Functional Free Energy Landscapes. Methods. 2018 May 29;: Authors: Byun JA, Melacini G Abstract Elucidating the molecular mechanism of disease-related mutations (DRMs) is a critical first step towards understanding the etiology of genetic disorders....	nmrlearner	Journal club	0	06-02-2018 12:52 PM
Characterization of Protein Kinase a Free Energy Landscape by NMR-Restrained Metadynamics Characterization of Protein Kinase a Free Energy Landscape by NMR-Restrained Metadynamics Publication date: 3 February 2017 Source:Biophysical Journal, Volume 112, Issue 3, Supplement 1</br> Author(s): Yingjie Wang, Carlo Camilloni, Jonggul Kim, Michele Vendruscolo, Jiali Gao, Gianluigi Veglia</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	02-03-2017 09:55 PM
[NMR paper] Exploring Free-Energy Landscapes of Intrinsically Disordered Proteins at Atomic Resolution Using NMR Spectroscopy. Exploring Free-Energy Landscapes of Intrinsically Disordered Proteins at Atomic Resolution Using NMR Spectroscopy. Exploring Free-Energy Landscapes of Intrinsically Disordered Proteins at Atomic Resolution Using NMR Spectroscopy. Chem Rev. 2014 Apr 11; Authors: Jensen MR, Zweckstetter M, Huang JR, Blackledge M PMID: 24725176	nmrlearner	Journal club	0	04-15-2014 10:38 AM
NMR Studies of the free Energy Landscape of Intrinsically Disordered Proteins in their free and Bound Forms NMR Studies of the free Energy Landscape of Intrinsically Disordered Proteins in their free and Bound Forms Publication date: 28 January 2014 Source:Biophysical Journal, Volume 106, Issue 2, Supplement 1</br> Author(s): Martin Blackledge</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	01-29-2014 12:50 AM
NMR-guided metadynamics of proteins [Biophysics and Computational Biology] NMR-guided metadynamics of proteins Granata, D., Camilloni, C., Vendruscolo, M., Laio, A.... Date: 2013-04-23 The use of free-energy landscapes rationalizes a wide range of aspects of protein behavior by providing a clear illustration of the different states accessible to these molecules, as well as of their populations and pathways of interconversion. The determination of the free-energy landscapes of proteins by computational methods is, however,... Read More PNAS: Number: 17	nmrlearner	Journal club	0	04-23-2013 08:37 PM
[NMR paper] Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Related Articles Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Proc Natl Acad Sci U S A. 2013 Apr 9; Authors: Granata D, Camilloni C, Vendruscolo M, Laio A Abstract The use of free-energy landscapes rationalizes a wide range of aspects of protein behavior by providing a clear illustration of the different states accessible to these molecules, as well as of their populations and pathways of interconversion. The...	nmrlearner	Journal club	0	04-11-2013 09:27 PM
Characterization of Free Energy Landscapes of Proteins using NMR Spectroscopy Characterization of Free Energy Landscapes of Proteins using NMR Spectroscopy 29 January 2013 Publication year: 2013 Source:Biophysical Journal, Volume 104, Issue 2, Supplement 1</br> </br> </br> </br></br>	nmrlearner	Journal club	0	02-03-2013 10:13 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