Hi,
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
=========================================================================== | 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: mensur@umich.edu | ===========================================================================
Hi,
We do have Windows version in the lab already, and it will be released as 6v2 in a few weeks.
Thanks, Bozidar
On 17/4/02 6:43 AM, "Mensur Dlakic" mensur@umich.edu wrote:
> Hi, > > 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 > > =========================================================================== > | 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: mensur@umich.edu | > =========================================================================== > >
Hello,
Libraries for main chain dihedral angles were updated , larger set of data and more detailed statistics, based on finer grid size and custom made Ramachandran plots for each residue. I do not know if mod v4 has it already but probably not.
In any case, it is always better to use the newest version, because many bugs have been fixed.
Andras Mensur Dlakic wrote: > > Hi, > > 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 > > =========================================================================== > | 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: mensur@umich.edu | > ===========================================================================
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Andras Fiser -
Bozidar Jerkovic -
Mensur Dlakic