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我叫江奕賢啦

2004年9月29日

maybe we can use http://i.moltalk.org/
instead of CSU
cause, sometimes CSU is not working.

Also, Moltalk will be quicker and more details.

choose "Find interface between two chains of a structure" in http://i.moltalk.org/
enter the pdb code,
when select chains, just select the same chain twice.

Done.

use
http://balabio.dcs.gla.ac.uk/tops/
to generate
http://www3.ebi.ac.uk/tops/ExplainDetailed.html
and you can easily compare things like

1bia

1gh4

2004年9月15日

For calculating Hydrogen Bond

HBPLUS, which is distributed with LIGPLOT: http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html

There's also HBOND, which comes with the JOY package:
http://www-cryst.bioc.cam.ac.uk/~joy/

they are free, but they all need Academic License which I can't apply individually, has to apply by UMDNJ.

for example, I want to know the H-Bonds in protein 1a2p, I go to

http://bioportal.weizmann.ac.il/oca-bin/csu?PDB_ID=1a2p

I found there's four sheet strands for each chain.
I click on "Strand 1" on "A sheet" (residue 96-99)
I'll go to this page
from this page, if there's a "+" sign under HB colume, I know there's a H-Bond.