for protein modeling, now there's some automatic modeling site.
PredictProtein (combind several methods) (1 day)
3D-pssm (Fold Recognition ) (10~20 min)
SWISS-MODEL (Homology modeling) (fastest, 1min)

the photoshop effect I applied on my BMW photo,
Stylize-Find Edges + Artistic-Cutout + ...

Net-Msmgr a MSN Perl Module

here has valuable info about msn, including lib, bot, client, protocol...


try talk to bot2k3@hotmail.com using MSN messenger!
it has several functions.

to use sybyl do 3d qsar on nci data:
put compounds in database,
change compounds' name to something doesn't content special char.
use "align database" to align compounds,
leave a core structure in molecular area will help you do the align.

search nci data and display in mdl mol format, then the core structure info can be get from the html source code, writing in MDL script.

you can use this command to get mol files.
wget -r --accept=mol http://129.43.27.140/tmp/hitscmUaRJ.html

you can use link like this to get GI50 data of NSC94600
http://129.43.27.140/cgi-bin/nci2.tcl/nci_download94600.tab?output=E_GI50&tablefmt=tabtable&op1=nsc&data1=94600&nomsg=0
or
http://cactus.nci.nih.gov/cgi-bin/nci2.tcl?op1=nsc&data1=94600&output=detail&conflist=-1&passid=&nomsg=1

sybyl servers in umdnj
achilles.umdnj.edu are pretty fast due to users usually use apollo and titan.

MDL mol file format works fine on NCI, so I planed to download MDL mol file then convert to sybyl mol2 file format. (maybe use openbabel)
tested by using babel to convert it. it works this way.
I don't know why files generated by nci can't be read by sybyl, ex: pdb not work, sybyl mol2 not work. mol not work, should be convert by using babel.

when babel don't work, put the files in a dos8 directory, ex: use d:\temp instead of d:\program files\...

now, the only thing left is, how can I align those compounds by the core substructure automatically.

It's a long time I didn't touch MAYA (a 3D modeling software for Computer Graphic)
now it has amazing features.
here are online tutorials via Streaming Videos

about MSN messenger:
Java MSN real status viewer (I can't get it work)
Triople can detect if a msn user is online of not. (web interface)
and you can even send message to an user who already blocked you by changing your nick name to a magic string.
(a special software to change nick name is required)

this "Online Status Indicator server" can let users know if someone is online or not.
but can't detect real status.

3D Minder cluster the anti-cancer compounds for you (need specific browser and java version +java3d)
Self-Organized Map cluster the anti-hiv compounds for you.

I think I should use -log(GI50) as the anti-cancer activity value for QSAR.
ref

I think I should use log(1/EC50)=?-log(EC50) as the anti-hiv activity value for QSAR.
ref

how to choose variables automatically in SAS (chinese)
how to fill missing values based on range and min. or use "proc mi"

this paper use JKlustor to cluster Anti-HIV compounds in NCI database.

use sql in sas

proc sql;
create table forweka as
select * from sasuser.all
where SEQN<200;
quit;
run;
quit;

Weka
tutorial about how to select variables

Weka can easily use CSV files.