One must remember that multiple sequences alignments are not just alignment of letters...they are amino acids with three dimensional (four if you count time) coordinates. The alignments can be very subjective and are best done in conjunction with a structural alignment of overlapping structures. Often it is best to choose PDB structures with the most diverse sequences in a particular structural family using VAST and/or DALI to align sequences, paying careful attention to alignment of prolines and glycines, knowing that loops are most always conserved, alpha helices are almost always alpha helices, strands almost always strands, and the connecting chain lengths may vary. Be patient :-)
Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: [email protected]
