

Hi Andy,

Standard rationale for getting 3D structures from sequence usually involve

1) database search of primary sequences (Brookhaven have some facilities 
   for this)

2) alignment of "best score" sequences (use FASTA, SOMAP etc.)

3) modelling of chunks or unknown sequence onto the 3D shapes of
   homologous proteins

4) annealing unknown coordinates to "stitch together" all the residues
   to make a final 3D model

5) refinement and minimization/dynamics

Quanta/CHARMm have , believe it or not, all of steps 1 to 5!

You can scan your structure database and get back "best hits". Use
FASTA to align multiple sequences (usually around 5 at once). Then
replace unknown coordinates bit by bit (based on the best homologous
structure/sequence). The annealing is done by CHARMm and you tweak the
refinement using rotamer libraries to place your sidechains. Then finish
off with CHARMm for the final minimization.

Let me know if you need any help in setting up your files etc. to
automate your database searching/alignments.

Richard

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