You would need to incorporate as much information you can find as possible to make the 'best' prediction of domain boundaries. Typically, I would put together all the following information in one multiple sequence alignment to design domain constructs for structural studies.
- Known structural homologs: exclude the flexible/disordered regions after visual inspection of the structures individually - Sequence homologs: include both orthologs (same protein from different genomes) and paralogs (different family members from the same genome) if possible to see where the ending conserved residues are. Keep all the conserved residues. - Secondary structure predictions: several servers are available now. I often use NPS (http://www.bioinf.manchester.ac.uk/dbbrowser/bioactivity/NPS2.html). These predictions typically have ~70% accuracy. For conflicting regions, I would choose results from PHD which is historically the best. - Consider hydrophobicity and complexity of the terminal sequences: stay away from terminal hydrophobic residues to improve solubility; exclude simple sequences such as SSSSPPP etc which would not have ordered structure. I have been thinking about building a bioinformatics web server for rational construct design. Please feel free to contact me if anyone is interested in joining me. Holly Jing @ Scripps, La Jolla ________________________________ > Date: Wed, 21 May 2008 00:05:08 +0100 > From: [EMAIL PROTECTED] > Subject: CCP4BB Digest - 19 May 2008 to 20 May 2008 (#2008-136) > To: CCP4BB@JISCMAIL.AC.UK > > CCP4BB Digest - 19 May 2008 to 20 May 2008 (#2008-136) > > Table of contents: > > * Primary literature for cyrocooling to mitigate radiation damage (2) > * Blake and Phillips 1962 > * Concatenated Crystal Screen Database (2) > * Right terminal residues for constructs. (3) > * Fwd: Right terminal residues for constructs. > * Maks file in HKL2000 (4) > _________________________________________________________________ Keep your kids safer online with Windows Live Family Safety. http://www.windowslive.com/family_safety/overview.html?ocid=TXT_TAGLM_WL_Refresh_family_safety_052008
