BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 11-24-2010, 10:03 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,492
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Refinement of NMR structures using implicit solvent and advanced sampling techniques.

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

Related Articles Refinement of NMR structures using implicit solvent and advanced sampling techniques.

J Am Chem Soc. 2004 Dec 15;126(49):16038-47

Authors: Chen J, Im W, Brooks CL

NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified force field and then refines these structures with implicit solvent using the REX method. We systematically examine the reliability and efficacy of this protocol using four proteins of various sizes ranging from the 56-residue B1 domain of Streptococcal protein G to the 370-residue Maltose-binding protein. Significant improvement in the structures was observed in all cases when refinement was based on low-redundancy restraint data. The proposed protocol is anticipated to be particularly useful in early stages of NMR structure determination where a reliable estimate of the native fold from limited data can significantly expedite the overall process. This refinement procedure is also expected to be useful when redundant experimental data are not readily available, such as for large multidomain biomolecules and in solid-state NMR structure determination.

PMID: 15584737 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Knowledge-based nonuniform sampling in multidimensional NMR
Knowledge-based nonuniform sampling in multidimensional NMR Abstract The full resolution afforded by high-field magnets is rarely realized in the indirect dimensions of multidimensional NMR experiments because of the time cost of uniformly sampling to long evolution times. Emerging methods utilizing nonuniform sampling (NUS) enable high resolution along indirect dimensions by sampling long evolution times without sampling at every multiple of the Nyquist sampling interval. While the earliest NUS approaches matched the decay of sampling density to the decay of the signal envelope, recent...
nmrlearner Journal club 0 06-06-2011 12:53 AM
[NMR paper] Sources of and solutions to problems in the refinement of protein NMR structures agai
Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force. Related Articles Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force. J Magn Reson. 2000 Oct;146(2):249-54 Authors: Kuszewski J, Clore GM It is often the case that a substantial number of torsion angles (both backbone and sidechain) in structures of proteins and nucleic acids determined by NMR are found in physically unlikely and...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR tweet] Nuclear magnetic resonance (NMR) is used in advanced medical imaging techniques; Magn
Nuclear magnetic resonance (NMR) is used in advanced medical imaging techniques; Magnetic Resonance Imaging (MRI). ??????????????????????? Published by ticca77 (??) on 2010-10-03T05:09:34Z Source: Twitter
nmrlearner Twitter NMR 0 10-03-2010 05:13 AM
[NMR paper] Conformational sampling by NMR solution structures calculated with the program DIANA
Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water. Related Articles Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water. Proteins. 1996 Mar;24(3):304-13 Authors: Berndt KD, Güntert P, Wüthrich K The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. J Biomol NMR. 1991 Sep;1(3):257-69 Authors: Mertz JE, Güntert P, Wüthrich K, Braun W A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. J Biomol NMR. 1991 Sep;1(3):257-69 Authors: Mertz JE, Güntert P, Wüthrich K, Braun W A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Related Articles Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins. 1990;8(4):377-85 Authors: Kim Y, Prestegard JH Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling...
nmrlearner Journal club 0 08-21-2010 10:48 PM
Random sampling in multidimensional NMR spectroscopy
Random sampling in multidimensional NMR spectroscopy Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 3 August 2010</br> Krzysztof, Kazimierczuk , Jan, Stanek , Anna, Zawadzka-Kazimierczuk , Wiktor, Ko?mi?ski</br> More...
nmrlearner Journal club 0 08-16-2010 03:50 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2017, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 07:09 PM.


Map