Related ArticlesHYPER: a hierarchical algorithm for automatic determination of protein dihedral-angle constraints and stereospecific C beta H2 resonance assignments from NMR data.
A new computer program, HYPER, has been developed for automated analysis of protein dihedral angle values and C beta H2 stereospecific assignments from NMR data. HYPER uses a hierarchical grid-search algorithm to determine allowed values of phi, psi, and chi 1 dihedral angles and C beta H2 stereospecific assignments based on a set of NMR-derived distance and/or scalar-coupling constraints. Dihedral-angle constraints are valuable for restricting conformational space and improving convergence in three-dimensional structure calculations. HYPER computes the set of phi, psi, and chi 1 dihedral angles and C beta H2 stereospecific assignments that are consistent with up to nine intraresidue and sequential distance bounds, two pairs of relative distance bounds, thirteen homo- and heteronuclear scalar coupling bounds, and two pairs of relative scalar coupling constant bounds. The program is designed to be very flexible, and provides for simple user modification of Karplus equations and standard polypeptide geometries, allowing it to accommodate recent and future improved calibrations of Karplus curves. The C code has been optimized to execute rapidly (0.3-1.5 CPU-sec residue-1 using a 5 degrees grid) on Silicon Graphics R8000, R10000 and Intel Pentium CPUs, making it useful for interactive evaluation of inconsistent experimental constraints. The HYPER program has been tested for internal consistency and reliability using both simulated and real protein NMR data sets.
Dihedral angle definition for proteins
Dihedral angle definition for proteins
This webpage lists the group of atoms that are uder every side-chain dihedral angle for proteins.
More...
nmrlearner
General
0
05-27-2011 10:44 PM
[NMR paper] Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy.
Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy.
Related Articles Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy.
J Am Chem Soc. 2005 Sep 21;127(37):12965-74
Authors: Andronesi OC, Becker S, Seidel K, Heise H, Young HS, Baldus M
It is shown that molecular structure and dynamics of a uniformly labeled membrane protein can be studied under magic-angle-spinning conditions. For this purpose, dipolar recoupling experiments...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] Automated NMR determination of protein backbone dihedral angles from cross-correlated
Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation.
Related Articles Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation.
J Biomol NMR. 2002 Apr;22(4):349-63
Authors: Kloiber K, Schüler W, Konrat R
The simultaneous interpretation of a suite of dipole-dipole and dipole-CSA cross-correlation rates involving the backbone nuclei 13Calpha, 1Halpha, 13CO, 15N and 1HN can be used to resolve the ambiguities associated with each individual...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] Determination of a molecular torsional angle in the metarhodopsin-I photointermediate
Determination of a molecular torsional angle in the metarhodopsin-I photointermediate of rhodopsin by double-quantum solid-state NMR.
Related Articles Determination of a molecular torsional angle in the metarhodopsin-I photointermediate of rhodopsin by double-quantum solid-state NMR.
J Biomol NMR. 2000 Jan;16(1):1-8
Authors: Feng X, Verdegem PJ, Edén M, Sandström D, Lee YK, Bovee-Geurts PH, de Grip WJ, Lugtenburg J, de Groot HJ, Levitt MH
We present a solid-state NMR study of metarhodopsin-1, the pre-discharge intermediate of the photochemical...
nmrlearner
Journal club
0
11-18-2010 09:15 PM
[NMR paper] Using neural network predicted secondary structure information in automatic protein N
Using neural network predicted secondary structure information in automatic protein NMR assignment.
Related Articles Using neural network predicted secondary structure information in automatic protein NMR assignment.
J Chem Inf Comput Sci. 1997 Nov-Dec;37(6):1086-94
Authors: Choy WY, Sanctuary BC, Zhu G
In CAPRI, an automated NMR assignment software package that was developed in our laboratory, both chemical shift values and coupling topologies of spin patterns are used in a procedure for amino acids recognition. By using a knowledge base of...
nmrlearner
Journal club
0
08-22-2010 05:08 PM
Precise structural determination of weakly binding peptides by utilizing dihedral ang
Abstract Structural determination of target-bound conformations of peptides is of primary importance for the optimization of peptide ligands and peptideâ??mimetic design. In the structural determination of weakly binding ligands, transferred nuclear Overhauser effect (TrNOE) methods have been widely used. However, not many distance constraints can be obtained from small peptide ligands by TrNOE, especially for peptides bound to a target molecule in an extended conformation. Therefore, for precise structural determination of weakly binding peptides, additional structural constraints are...
nmrlearner
Journal club
0
08-14-2010 04:19 AM
NOESY signals and chi2 dihedral angle
Hello out there! I have a question about the intensity of NOESY correlation signals and the chi2 dihedral angle. The more intense the NOE signals are, the closer the distance between the two nuclei, right? So, if two beta protons have close to the same NOE intensity on the NOESY, which can be described as medium intensity, what does that say about the conformation around the chi2 dihedral angle.........?
HYPER: a hierarchical algorithm for automatic determination of protein dihedral-angle
Linear Mode
