RDC applications:
1) Small molecules. RDCs can be used to determine the molecular absolute configurations. For instance, one molecule might be R or S configurations, however, the C-H bond orientation will be different in these two configurations, thus allows the differentiation by RDCs. Remember, RDC is sensitive to internuclear vector orientation and distance. You may need at least 11 RDC measurements and the proposed molecular structures a priori.
2) Biomolecules. Structure refinement. That's to say, a low resolution structure has been determined either from NMR NOE or X-ray, the application of RDC will greatly boost the resolution as it provides an accurate and quantitative description over the vector orientation and distance. While NOE can only provide the semi-quantitative distance information
3) Protein-ligand interaction, i.e., transferred RDCs.
4) Dynamics
For PALES,
If you have the protein pdb structure, you may predict how the protein will align in the the specific media, so far only in Bicelle and Phage. However the accuracy of the prediction of electrostatic interactions is still far away from satisfactory.
Useage, in Unix/Linux command line
pales -Dtest.pdb
where test.pdb will be replaced by your structure.
If you have the RDC measurements, PALES will calculate the alignment tensors and the back-calculated RDCs. PALES provides a nice example, so you may run that first. And make sure the file format of your RDCs (text file) conform with PALES.
原文由 yohanna 发表:
1. 有没有人懂 residual dipolar couplings 在分子及结构分析方面的应用?
2. 有人知道 PALES 软件 到底怎么用啊
http://www.mpibpc.mpg.de/groups/griesinger/zweckstetter/_links/software_pales.htm
我看了好久,还是看不明白,这个 Prediction of molecular alignment from structure using the PALES software.
求助!
谢谢大家!