Hi - we normally use:
http://toolkit.tuebingen.mpg.de/hhpred together with: http://toolkit.tuebingen.mpg.de/quick2_d Both routines have a nice interface and a very sensitive and novel CS-Blast algorithm which can be used/integrated into the search. Best wishes Kornelius On Mon, 30 Mar 2009 14:11:02 +0100 Haridasan Namboodiri <vnambood...@locuspharma.com> wrote: > Hello > > I am designing a protein construct for structural biology. It is a protein > kinase > which has not been crystallized earlier. I was comparing the kinase domains > of > other closely related family members characterized biochemically vs > crystallization constructs. For crystallography constructs, there are > different > stretches of amino acid residues particularly at the N-terminus (some contain > extra 2-5 residues while others have 15-20 residues. > > My question: Is there a rational way of designing exact constructs one > would propose to make, eg., by a sequence alignment showing nearest > homology neighbors that guided construct design etc.. > > > Sincerely > Hari > > Haridasan V. M. Namboodiri, PhD > Scientist-Structural Biology > Locus Pharmaceuticals, Inc. > Four Valley Square > 512 Township Line Road > Blue Bell, PA 19422 > email: vnambood...@locuspharma.com > Ph: 215-358-2012 > Fax: 215-358-2020 ---------------------------------------------- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349
