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
Optimization of amino acid type-specific (13)C and (15)N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.
Optimization of amino acid type-specific (13)C and (15)N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.
Optimization of amino acid type-specific (13)C and (15)N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.
J Biomol NMR. 2010 Dec 18;
Authors: Hefke F, Bagaria A, Reckel S, Ullrich SJ, Dötsch V, Glaubitz C, Güntert P
We present a computational method for finding optimal labeling patterns for the backbone...
nmrlearner
Journal club
0
12-21-2010 01:00 PM
Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm
Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm
Abstract We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273â??6279 (1982)), types of amino acids are labeled with 13C or/and 15N such that cross peaks between 13CO(i â?? 1) and 15NH(i) result only for pairs...
nmrlearner
Journal club
0
12-21-2010 02:14 AM
[NMR paper] GANA--a genetic algorithm for NMR backbone resonance assignment.
GANA--a genetic algorithm for NMR backbone resonance assignment.
Related Articles GANA--a genetic algorithm for NMR backbone resonance assignment.
Nucleic Acids Res. 2005;33(14):4593-601
Authors: Lin HN, Wu KP, Chang JM, Sung TY, Hsu WL
NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic algorithm to automatically perform backbone resonance assignment with a high degree of precision and recall....
nmrlearner
Journal club
0
11-24-2010 11:14 PM
[NMR paper] More reliable protein NMR peak assignment via improved 2-interval scheduling.
More reliable protein NMR peak assignment via improved 2-interval scheduling.
Related Articles More reliable protein NMR peak assignment via improved 2-interval scheduling.
J Comput Biol. 2005 Mar;12(2):129-46
Authors: Chen ZZ, Lin G, Rizzi R, Wen J, Xu D, Xu Y, Jiang T
Protein NMR peak assignment refers to the process of assigning a group of "spin systems" obtained experimentally to a protein sequence of amino acids. The automation of this process is still an unsolved and challenging problem in NMR protein structure determination. Recently,...
nmrlearner
Journal club
0
11-24-2010 11:14 PM
[NMR paper] A general NMR method for rapid, efficient, and reliable biochemical screening.
A general NMR method for rapid, efficient, and reliable biochemical screening.
Related Articles A general NMR method for rapid, efficient, and reliable biochemical screening.
J Am Chem Soc. 2003 Nov 26;125(47):14620-5
Authors: Dalvit C, Ardini E, Flocco M, Fogliatto GP, Mongelli N, Veronesi M
High-throughput screening is usually the method of drug-lead discovery. It is now well accepted that, for a functional assay, quality is more important than quantity. The ligand-based or protein-based NMR screening methodologies for detecting compounds...
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] An efficient branch-and-bound algorithm for the assignment of protein backbone NMR pe
An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.
Related Articles An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.
Proc IEEE Comput Soc Bioinform Conf. 2002;1:165-74
Authors: Lin G, Xu D, Chen ZZ, Jiang T, Wen J, Xu Y
NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH
Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH
Jochen Volk, Torsten Herrmann and Kurt Wüthrich
Journal of Biomolecular NMR; 2008; 41(3); pp 127 - 138
Abstract:
MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics...
A New Algorithm for Reliable and General NMR Resonance Assignment
Linear Mode
