Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
nmrlearner
Journal club
0
07-15-2011 09:10 PM
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
4D prediction of protein 1H chemical shifts
4D prediction of protein 1H chemical shifts
Abstract A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6â??7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins...
nmrlearner
Journal club
0
01-09-2011 12:46 PM
[KPWU blog] Install Rosetta-3.1 and CS-Rosetta on Mac OS 10.6
Install Rosetta-3.1 and CS-Rosetta on Mac OS 10.6
A note of my installation in the last 3 days. Machine: iMac 3.06 GHz, core i3, 4 GB Ram , OS 10.6.4 Part A –Rosetta 3.1 First download Rosetta 3.1, all the bundle stuff. –uncompress the bundle file, and keep uncompress the all .tgz files Then download corrections for rosetta_source at here: http://zinc.ucsf.edu/~colin/snow_leopard_tools.tar.gz (see this http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=227&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
12-24-2010 03:24 PM
Structure Calculation Using CS-DP ROSETTA from NESG Wiki
Structure Calculation Using CS-DP ROSETTA
This is a copy of instructions for CS-DP Rosetta from NESG Wiki that was created on 8/20/19. Please go to the original post at http://www.nmr2.buffalo.edu/nesg.wiki/Structure_Calculation_Using_CS-DP_ROSETTA
for a more up-to-date version.
Introduction
The CS-DP-Rosetta approach merges the ideas of model generation using CS-Rosetta with model filtering by agreement to NOESY data via the DP-score from the RPF program to generate high accuracy protein structures. This hybrid approach uses both local backbone chemical shift data...
CS-ROSETTA: System for chemical shifts based protein structure prediction using ROSETTA
Linear Mode
