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

Go Back   BioNMR > Software > Molecular modeling software > NMR structure calculation
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 03-23-2005, 08:43 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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

Module 1.0 - interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings.

Download page

Manual

Reference


Program description from its website:

Module is a program developed to allow the determination of alignment tensor parameters for individual or multiple domains in macromolecules from residual dipolar couplings and to facilitate their manipulation to construct low-resolution models of macromolecular structure.

For multi-domain systems the program determines the relative orientation of individual structured domains, and provides graphical user-driven rigid-body modeling of the different modules relative to the common tensorial frame.

Translational freedom in the common frame, and equivalent rotations about the diagonalized (x,y,z) axes, are used to position the different modules in the common frame to find a model in best agreement with experimentally measured couplings alone or in combination with additional experimental or covalent information.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set.
Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set. Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set. J Mol Biol. 2011 May 23; Authors: Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A The CS-RDC-NOE Rosetta program was used to generate the solution structure of a 27-kDa fragment of the Escherichia coli BamC protein from a limited set of NMR data. The BamC protein is a component of the essential five-protein ?-barrel assembly machine in E. coli. The...
nmrlearner Journal club 0 06-01-2011 02:30 PM
[NMR paper] Characterization of the carboxylate delivery module of transcarboxylase: following sp
Characterization of the carboxylate delivery module of transcarboxylase: following spontaneous decarboxylation of the 1.3S-CO2- subunit by NMR and FTIR spectroscopies. Related Articles Characterization of the carboxylate delivery module of transcarboxylase: following spontaneous decarboxylation of the 1.3S-CO2- subunit by NMR and FTIR spectroscopies. Biochemistry. 2002 Feb 19;41(7):2191-7 Authors: Rivera-Hainaj RE, Pusztai-Carey M, Venkat Reddy D, Choowongkomon K, Sönnichsen FD, Carey PR Transcarboxylase (TC) is a multisubunit enzyme that...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Characterization of the EGF-like module pair 3-4 from vitamin K-dependent protein S u
Characterization of the EGF-like module pair 3-4 from vitamin K-dependent protein S using NMR spectroscopy reveals dynamics on three separate time scales and extensive effects from calcium binding. Related Articles Characterization of the EGF-like module pair 3-4 from vitamin K-dependent protein S using NMR spectroscopy reveals dynamics on three separate time scales and extensive effects from calcium binding. Biochemistry. 2000 Dec 26;39(51):15742-56 Authors: Muranyi A, Evenäs J, Stenberg Y, Stenflo J, Drakenberg T Protein S, a cofactor of...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] An NMR assignment module implemented in the Gifa NMR processing program.
An NMR assignment module implemented in the Gifa NMR processing program. Related Articles An NMR assignment module implemented in the Gifa NMR processing program. Bioinformatics. 1998;14(7):624-31 Authors: Malliavin TE, Pons JL, Delsuc MA MOTIVATION: Peptide and protein structures are determined daily using NMR spectroscopy. Assignment of the NMR spectra is an important step within the procedure and is usually the limiting one. Computer-aided assignment tools should be user friendly with open architecture to communicate with other programs...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data
Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. J Mol Biol. 1995 Apr 7;247(4):689-700 Authors: van Tilborg MA, Bonvin AM, HÃ¥rd K, Davis AL, Maler B, Boelens R, Yamamoto KR, Kaptein R The solution structure of the glucocorticoid...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain
Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy. Related Articles Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy. Biochemistry. 1994 Nov 22;33(46):13531-9 Authors: Wittekind M, Mapelli C, Farmer BT, Suen KL, Goldfarb V, Tsao J, Lavoie T, Barbacid M, Meyers CA, Mueller L NMR spectroscopy has been used to characterize the protein-protein interactions between the mouse Grb2 (mGrb2) N-terminal...
nmrlearner Journal club 0 08-22-2010 03:29 AM
[Question from NMRWiki Q&A forum] MODULE for RDC
MODULE for RDC I'm trying to analyze my RDC data using Module. But I'm using a crystal structure instead of NMR. Can somebody pls advise me on how to do this? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 08-22-2010 02:30 AM
[NMR paper] Solution structure and orientation of the transmembrane anchor domain of the HIV-1-en
Solution structure and orientation of the transmembrane anchor domain of the HIV-1-encoded virus protein U by high-resolution and solid-state NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Solution structure and orientation of the transmembrane anchor domain of the HIV-1-encoded virus protein U by high-resolution and solid-state NMR spectroscopy. Biochemistry. 1999 Apr 20;38(16):5272-82 Authors: Wray V, Kinder R, Federau T, Henklein P, Bechinger B, Schubert U The...
nmrlearner Journal club 0 08-21-2010 04:03 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 - 2024, 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 11:08 AM.


Map