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 08-22-2010, 03:50 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,586
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 Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-

Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain.

Related Articles Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain.

J Biomol NMR. 1995 Nov;6(3):294-305

Authors: Morikawa S, Ogata K, Sekikawa A, Sarai A, Ishii S, Nishimura Y, Nakamura H

The solution structure of a specific DNA complex of the minimum DNA-binding domain of the mouse c-Myb protein was determined by distance geometry calculations using a set of 1732 nuclear Overhauser enhancement (NOE) distance restraints. In order to determine the complex structure independent of the initial guess, we have developed two different procedures for the docking calculation using simulated annealing in four-dimensional space (4D-SA). One is a multiple-step procedure, where the protein and the DNA were first constructed independently by 4D-SA using only the individual intramolecular NOE distance restraints. Here, the initial structure of the protein was a random coil and that of the DNA was a typical B-form duplex. Then, as the starting structure for the next docking procedure, the converged protein and DNA structures were placed in random molecular orientations, separated by 50 A. The two molecules were docked by 4D-SA utilizing all the restraints, including the additional 66 intermolecular distance restraints. The second procedure comprised a single step, in which a random-cell protein and a typical B-form DNA duplex were first placed 70 A from each other. Then, using all the intramolecular and intermolecular NOE distance restraints, the complex structure was constructed by 4D-SA. Both procedures yielded the converged complex structures with similar quality and structural divergence, but the multiple-step procedure has much better convergence power than the single-step procedure. A model study of the two procedures was performed to confirm the structural quality, depending upon the number of intermolecular distance restraints, using the X-ray structure of the engrailed homeodomain-DNA complex.

PMID: 8520221 [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
[NMR paper] Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli m
Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system. Related Articles Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system. J Biol Chem. 2005 May 27;280(21):20775-84 Authors: Williams DC, Cai M, Suh JY, Peterkofsky A, Clore GM The solution structure of the 48-kDa IIA(Man)-HPr complex of the mannose branch of the Escherichia coli phosphotransferase system has been solved by NMR using conjoined rigid body/torsion...
nmrlearner Journal club 0 11-24-2010 11:14 PM
NMR Solution Structure of a DNA-Actinomycin D Complex Containing a Non-Hydrogen-Bondi
NMR Solution Structure of a DNA-Actinomycin D Complex Containing a Non-Hydrogen-Bonding Pair in the Binding Site Shannen L. Cravens, Alyssa C. Navapanich, Bernhard H. Geierstanger, Deborah C. Tahmassebi and Tammy J. Dwyer http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107575f/aop/images/medium/ja-2010-07575f_0011.gif Journal of the American Chemical Society DOI: 10.1021/ja107575f http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/tQROiStkm5c
nmrlearner Journal club 0 11-23-2010 07:10 AM
[NMR paper] NMR solution structure of a complex of calmodulin with a binding peptide of the Ca2+
NMR solution structure of a complex of calmodulin with a binding peptide of the Ca2+ pump. Related Articles NMR solution structure of a complex of calmodulin with a binding peptide of the Ca2+ pump. Biochemistry. 1999 Sep 21;38(38):12320-32 Authors: Elshorst B, Hennig M, F÷rsterling H, Diener A, Maurer M, Schulte P, Schwalbe H, Griesinger C, Krebs J, Schmid H, Vorherr T, Carafoli E The three-dimensional structure of the complex between calmodulin (CaM) and a peptide corresponding to the N-terminal portion of the CaM-binding domain of the...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Determination of the NMR structure of the complex between U1A protein and its RNA pol
Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. Related Articles Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. J Biomol NMR. 1998 Jan;11(1):59-84 Authors: Howe PW, Allain FH, Varani G, Neuhaus D RNA-protein recognition is critical to post-transcriptional regulation of gene expression, yet poorly understood at the molecular level. The relatively slow progress in understanding this important area of...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1
NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Related Articles NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science. 1993 Jul 23;261(5120):438-46 Authors: Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM The three-dimensional solution structure of a complex between the DNA binding domain of the chicken erythroid transcription factor GATA-1 and its cognate DNA site has been determined with multidimensional...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Sequence-specific 1H-NMR assignment and determination of the secondary structure of b
Sequence-specific 1H-NMR assignment and determination of the secondary structure of bovine heart fatty-acid-binding protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Sequence-specific 1H-NMR assignment and determination of the secondary structure of bovine heart fatty-acid-binding protein. Eur J Biochem. 1992 Dec 15;210(3):901-10 Authors: L├╝cke C, Lassen D, Kreienkamp HJ, Spener F, R├╝terjans H The nearly complete...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR paper] The three-dimensional structure of guanine-specific ribonuclease F1 in solution deter
The three-dimensional structure of guanine-specific ribonuclease F1 in solution determined by NMR spectroscopy and distance geometry. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles The three-dimensional structure of guanine-specific ribonuclease F1 in solution determined by NMR spectroscopy and distance geometry. Eur J Biochem. 1992 Aug 15;208(1):41-51 Authors: Nakai T, Yoshikawa W, Nakamura H, Yoshida H Two-dimensional 1H-NMR...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR paper] Sequence-specific 1H NMR assignments and determination of the secondary structure for
Sequence-specific 1H NMR assignments and determination of the secondary structure for the activation domain isolated from pancreatic procarboxypeptidase B. Related Articles Sequence-specific 1H NMR assignments and determination of the secondary structure for the activation domain isolated from pancreatic procarboxypeptidase B. Biochemistry. 1990 Aug 14;29(32):7515-22 Authors: Vendrell J, Wider G, Avil├ęs FX, W├╝thrich K Nearly complete sequence-specific 1H NMR assignments are presented for amino acid residues 3-81 in the 81-residue globular...
nmrlearner Journal club 0 08-21-2010 11:04 PM


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 06:05 PM.


Map