structural biology - RMSD during conformational transition in proteins

When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved both with X-ray and NMR. The average root-mean-square deviation (RMSD) between NMR and Xray structures is 1.4Å (max. 3.6Å), and the average RMSD between different NMR structures for same protein is 0.4Å (max. 1.3Å). I've checked some proteins studied in this paper, and they are mostly within 100–200 residues long.However, there are plenty of papers (e...Read more

structural biology - Which factors besides the thermodynamic stability are important for the hairpin in intrinsic transcription termination?

Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based on the thermodynamic stability of the sequence. The GC-rich stable hairpin together with the destabilizing U-repeat supposedly destabilize the binding of the polymerase enough to cause it to disassociate from the template.What I'm looking for are specific requirements on the termination sequences that are not based on thermodynamics. Are there any ...Read more

structural biology - Determine if two molecule structures are the same molecule (perhaps in different conformations)?

I have two .pdb files describing two (small ligand) molecular structures. I need to determine if these two pdbs describe the same molecule, perhaps in different spatial conformations. Is there a program, or a combination of tools that will allow me to do this?Moreover, if the two pdbs are determined to be from the same molecule, it could be that the atoms are in different orders. So I also need a way to identify the atoms in one PDB with the atoms in the other PDB.I am dealing with thousands of pdbs, so I need an automatic way to do this compar...Read more