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Loop modeling: old vs. new


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:         |