Falcipain docking

[Jean-Claude Bradley]

Following up on my post on our falcipain collaboration,

http://usefulchem.blogspot.com/2007/08/falcipain-collaboration.html

 

Rajarshi has posted this:

 

Not a problem to set of more docking runs, though I might not get to it before the end of this month, after I get back from the ACS

But looking at the PDB structure seems to indicate that it's a protein-protein interaction. As a result the binding site seems to be very broad and shallow, which could be problematic. It's definitely interesting, since this'll be the first time I'm doing a PPI

The paper notes 3 catalytic residues, so I assume that that would be the focus of a docking protocol.

But I can certainly set of the runs


--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University

http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com

[jcb]

Rajarshi has completed the docking runs on falcipain-2.
Khalid/Rikesh please look at the top 10 for each binding site to see
if we can make any of them with the starting materials that have
already arrived.

A summary is on the wiki
http://usefulchem.wikispaces.com/D-EXP012

Details from Rajarshi:

I've run the docking runs on the combiugi library against 1YVB - I've
provided a brief summary and links to ranked score files.

As I noted, the exact binding site is not clear, so I selected two
different sites based on visual inspection and a PPI prediction
server (SPPIDER).

I haven't linked to actual 3D poses but can make them available if
required.

http://rguha.ath.cx/~rguha/cicc/fpdock/

(also, note that I haven't applied any drug-like filters to the combi
library, so hits may or may not be drug or lead like, but it's
trivial to run it on the results)

On Aug 9, 11:32 am, "Jean-Claude Bradley"
<jeanclaude.brad...@gmail.com> wrote:
> Following up on my post on our falcipain collaboration,http://usefulchem.blogspot.com/2007/08/falcipain-collaboration.html

[Khalid Mirza]

We will be unable to make any one the either Top 10 compounds due to the lack of starting materials.

On 9/23/07, jcb < jeanclaud...@gmail.com> wrote:

Rajarshi has completed the docking runs on falcipain-2.
Khalid/Rikesh please look at the top 10 for each binding site to see
if we can make any of them with the starting materials that have
already arrived.

A summary is on the wiki
http://usefulchem.wikispaces.com/D-EXP012

Details from Rajarshi:

I've run the docking runs on the combiugi library against 1YVB - I've
provided a brief summary and links to ranked score files.

As I noted, the exact binding site is not clear, so I selected two
different sites based on visual inspection and a PPI prediction
server (SPPIDER).

I haven't linked to actual 3D poses but can make them available if
required.

http://rguha.ath.cx/~rguha/cicc/fpdock/

(also, note that I haven't applied any drug-like filters to the combi
library, so hits may or may not be drug or lead like, but it's
trivial to run it on the results)

On Aug 9, 11:32 am, "Jean-Claude Bradley"
<jeanclaude.brad...@gmail.com> wrote:

> Following up on my post on our falcipain collaboration, http://usefulchem.blogspot.com/2007/08/falcipain-collaboration.html

>
> Rajarshi has posted this:
>
> Not a problem to set of more docking runs, though I might not get to it
> before the end of this month, after I get back from the ACS
>
> But looking at the PDB structure seems to indicate that it's a
> protein-protein interaction. As a result the binding site seems to be very
> broad and shallow, which could be problematic. It's definitely interesting,
> since this'll be the first time I'm doing a PPI
>
> The paper notes 3 catalytic residues, so I assume that that would be the
> focus of a docking protocol.
>
> But I can certainly set of the runs
>
> --
> Jean-Claude Bradley, Ph. D.
> E-Learning Coordinator for the College of Arts and Sciences
> Associate Professor of Chemistry
> Drexel University
>
> http://drexel-coas-elearning.blogspot.comhttp://drexel-coas-talks-mp3-podcast.blogspot.com/http://usefulchem.blogspot.com

Khalid Mirza
Graduate Student
The Bradley Research Group
Department of Chemistry
Drexel University
usefulchem.wikispaces.com

[Jean-Claude Bradley]

How about the top 100?