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