Subject: Re: CCL:Nativeness RMSD

From: Eric Bennett <ericb{at}pobox.com>
Date: Mon, 04 Oct 2004 10:36:58 -0500

Yong Liang Yang wrote:

> Dear Colleagues:
>
>      I would like to calculate the nativeness RMSD of docked
> structures from a small molecules database with the native
> ligand (reference structure) from crystal structure. In another word,
> I want to calculate RMSD of two different structures without translating
> or changing the orientation of second structure.
>
>      However, most RMSD algorithms try to translate the orientation of
> second structure and minimize the distance. Could someone recommend
> some packages or codes which could calculate nativeness RMSD? Many
> thanks and appreciate it. (I have posted this topic on Autodock list)

There's almost certainly a better way, but you can trick ProFit into 
doing this:
http://acrmwww.biochem.ucl.ac.uk/software/

In ProFit you use the "ZONE" command to specify the range of residues to 
fit and you can use an "ATOMS" command to narrow the fitting to certain 
kinds of atoms (CA to fit only alpha carbons for example).  You have to 
fit before you get an RMS.  But after you fit, you can change the atoms 
used to calculate the RMS using the "RATOMS" command and you will get a 
new RMS calculated *without* translating the atoms.

So to trick ProFit you'd have to add a couple dummy atoms with identical 
coordinates to each structure and do a "superimpose" that has no effect 
(because the atoms are already in identical positions) using just those 
atoms.  Since ZONE has to be over more than one residue, you'd have to 
have one of your dummy atoms in a residue numbered differently from the 
ligand. Then calculate the RMS over all the other atoms using RATOMS; no 
new superposition will be performed.  You might want to give your dummy 
atoms a unique PDB atom name so you can select just those atoms with the 
ATOMS command. 

While this is somewhat clunky, if you are handy with unix shell scripts 
you can automate this process to add the dummy atoms AND do the actual 
fitting in ProFit since ProFit is a command line program.  You will have 
to use the -h option for ProFit if your ligand is defined using HETATM 
records.

If you happen to have access to the commercial Maestro interface from 
Schrodinger, it will also calculate RMS without superposition if you 
check the "Calculate in place" box.  This is much easier than playing 
games with ProFit but you have to buy the software.

-- 
Eric Bennett, Center for Drug Design, U of Minnesota

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