cleaning data in sas

for example:
Deleting variables that have missing values on any observation
Delete variables that have only missing values

3D Mind will cluster your compounds for you.
and it can also show you what else are in that cluster.

go into 3D Mind tools and use node 23+18 (cluster 16.8 + 17.9)
or node 13+11+7+3+...

or you can search by SMILE string: "C1CC3=C(CO1)CN2CC5=C(C2=C3)N=C4C=CC=CC4=C5" here

here's a paper uses NCI's anticancer database to do QSAR

found a pretty good entry to find cancer screen data from nci
for aids screen data get compouds here then get activity here or see structures here

what is GI50 TGI LC50 in nci database

you can use online tools: NCI 3DMiner or Enhanced NCI Database Browser to search compounds list here, then you can easily compare those compounds.

after you saw some substructure shared by all the structures above,
and got more structures by substructure search.
you can use this page to see there activies.

Ward in JKlustor can work with GenerateMD then you can Clustering using Pharmacophore Fingerprints.
Ref: example section of this page

you can use Jarp and Ward in JKlustor
to cluster the compounds based on NCI's data
ref: http://www.chemaxon.com/conf/Eurocombi_poster_Ltr.pdf

there's a freeware like ghost
called g4u (ghost for unix)
works in a floppy disk and can upload harddisk image to a ftp server. and dump to another computer's harddisk.

I think I can find a drug for AIDS here.(example)

and it will gives me several similar compounds and CAS#

then I can use those CAS# to search activity data here

for Cancer, use these Drugs list1 Drug List 2 and Acitivity

PS: if interested in anti-cancer plants, you can find it and compounts it produced here or here.

Oops, I WAS planing to do an automated QSAR program for binf7592
but after I read Ch.5.3.3 in the paper "Structure Database" teacher gave us on 10/20.
I noticed there are several tools exist. "Catalyst" and "APEX"
details about catalyst and apex

drug activity data can be obtained from here for binf7592 project

other activity database for future job can be obtained here

we know SMILES is not Unique.
but it's very easy to Translate to unique smiles.

Grail has socket interface
ref original
detail (official)

use meme to find motifs
./meme ../../markfilter/shrtincor.fa -protein -mod zoops -nmotifs 20 -minsites 2 -maxsites 5 -minw 3 -maxw 50 -evt 10000 -time 7200 -maxsize 60000 -nostatus -maxiter 25 > output.html

use meta-meme to make hmm
./mhmm -meme ../../../meme.3.0.4/bin/output.html > test.mhmm

test sequences using that hmm
./mhmmscan -hmm test.mhmm -seq ../../../markfilter/shrtcor.fa 2>/dev/null | more

META-MEME seems good for my HMM engine,
but after some research, maybe MEME will sute me more.
it can find motifs for me in the sequences.
and of course, if you want HMM, you are one button away!

seems I can use it on super computer, but still slow...

I think I might use HMMER or SAM or HTK or GHMM as my HMM engine.
and train the model by using both positive exon-intron group and nagtive exon-intron group.

web interface for:
convert between HMMER and SAM.
HMMER
SAM

using netcat to scan your computer ports:
nc -v -z 192.168.1.102 1-9999
will scan port 1~port 9999 for you without delay.

Hansch Analysis (2D -QSAR), Free-Wilson, 3D QSAR (chinese)

Hammett equation, σ-constant...
Octanol-Water Partition Coefficient