Has anyone done a real comparison between standalone loop refinment procedures in v4.x versus v6.x? Or, for that matter, is any objective benchmarking available that compares the two versions? I am one of those people who don't like to update the software that already works well, and one thing that would definitely motivate me to do so is the improvement in loop procedures. On a related note, is there any word about the DOS/Windows version of MODELLER?
What is the lowest target/template identity that has still produced a good model of a 80+ residues protein? I am hoping to hear real examples and not only a generic answer ("depends on template resolution, alignment quality..."). I have made good models in a 10-20% range of indentities, but is it realistic to expect a good model with < 10% identity even after the iterative realignment? I am often tempted to model proteins falling into below 10% category but haven't done it more than 2-3 times, always with disappointing results.
Thanks for your time. May your objectives be high and your objective function low,
=========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: firstname.lastname@example.org | ===========================================================================