Hi, I'm looking for a program to improve a low homology sequence alignment using the known (but unpublished) structure of one of the sequences. Programs like Verify3D and CPROF (Eisenberg's lab) generate the environmental profile of a structure, but then how do I apply that to other sequences to improve an alignment.
This request is compounded by the structural size of the sequence, 2100 amino acids containing some 70 helices (very repetative). Hence using a starting alignment is a good idea. THREADER won't build a TDB file (target file) for something this big. I guess we could do it in sections and then thread small portions of the weak homologs individually. We've hit a variety of errors with the TDB server. Other "threader" servers only use PDB archives, not new structures. any ideas. Heidi
