Hitchens TK, Lukin JA, Zhan Y, McCallum SA, Rule GS.
Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
J Biomol NMR. 2003 Jan;25(1):1-9.
A general-purpose Monte Carlo assignment program has been developed to aid in the assignment of NMR resonances from proteins. By virtue of its flexible data requirements the program is capable of obtaining assignments of both heavily deuterated and fully protonated proteins. A wide variety of source data, such as inter-residue scalar connectivity, inter-residue dipolar (NOE) connectivity, and residue specific information, can be utilized in the assignment process. The program can also use known assignments from one form of a protein to facilitate the assignment of another form of the protein. This attribute is useful for assigning protein-ligand complexes when the assignments of the unliganded protein are known. The program can be also be used as an interactive research tool to assist in the choice of additional experimental data to facilitate completion of assignments. The assignment of a deuterated 45 kDa homodimeric Glutathione-S-transferase illustrates the principal features of the program.
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers
Abstract We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly 15N,13C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes...
nmrlearner
Journal club
0
06-30-2011 05:01 AM
[NMR paper] RFAC, a program for automated NMR R-factor estimation.
RFAC, a program for automated NMR R-factor estimation.
Related Articles RFAC, a program for automated NMR R-factor estimation.
J Biomol NMR. 2000 Jun;17(2):137-51
Authors: Gronwald W, Kirchhöfer R, Görler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR
A computer program (RFAC) has been developed, which allows the automated estimation of residual indices (R-factors) for protein NMR structures and gives a reliable measure for the quality of the structures. The R-factor calculation is based on the comparison of experimental and simulated 1H...
nmrlearner
Journal club
0
11-18-2010 09:15 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
what is the best program for assignment?
Hi I'm a student who would like to know which is the best program for assignment, (CARA?) in particulary one which is very easy to use. thanx!!! :confused:
Gianlu83
NMR software
2
02-09-2009 11:30 AM
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
Alexander Lemak, Carlos A. Steren, Cheryl H. Arrowsmith and Miguel Llinás
Journal of Biomolecular NMR; 2008; 41(1); pp 29 - 41
Abstract:
ABACUS is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic...
Mikey
Journal club
0
08-14-2008 12:37 AM
automated backbone assignment
Can anyone suggest me a most commonly used and worthful software for automated backbone assignment of triple labeled proteins.
Thanks.
sarun
NMR Questions and Answers
2
03-30-2007 03:21 PM
CARA: a new program for NMR assignment
The following message was posted by damberge on old PostNuke of Bionmr.com
"CARA is a new program being developed at the ETH for computer-aided resonance assignment. It has dedicated tools along with a well organized database which allow for efficient assignment. A scripting language and many user scripts are available (including one to automate assignments). All major platforms are available (Windows, Linux, Mac, SGI, Sun) and it is free. It can be downloaded at:
www.nmr.ch "
Linear Mode
