Re: [ccp4bb] off-topic: binding site comparison

2015-02-02 Thread Sarah Barelier 
Dear Daisuke,

Thank you for your answer.
I was looking at the 3D-SURFER server, it looks great. I'm only trying to
compare pairs (or sometimes triplets) of proteins though. Is there a way to
use 3D-SURFER for that purpose? And would it give me a 3D structural
alignment of the binding sites?

Thanks,

Sarah

On Fri, Oct 31, 2014 at 4:46 PM, Daisuke Kihara dkih...@purdue.edu wrote:

 Dear Sarah,

 we don't have a server for you to quickly use but our lab has methods for
 alignment-free binding sites comparison by comparing pocket surface shape,
 named Pocket-Surfer and Patch-Surfer.

 These are literature:
 http://www.ncbi.nlm.nih.gov/pubmed/20455259
 http://www.ncbi.nlm.nih.gov/pubmed/22275074

 http://bioinformatics.oxfordjournals.org/content/early/2014/10/29/bioinformatics.btu724.abstract

 If you are interested, I am happy to discuss what we can do for your
 problem.
 Sincerely,
 Daisuke
 
 Daisuke Kihara, Ph.D.
 Professo
 Department of Biological Sciences/Computer Science
 Purdue University
 West Lafayette, IN 47907
 http://kiharalab.org Tel: 1-765-496-2284



 On Fri, Oct 31, 2014 at 3:48 PM, Sarah Barelier 
 sarah.barel...@blur.compbio.ucsf.edu wrote:

 Dear all,
 I'm sorry, this is a bit off-topic. I'm looking for a tool to compare
 pairs of binding sites.
 It doesn't need to be high-throughput, since I'll only be comparing ~100
 pairs, but I'd like it to be robust and, more importantly,
 alignment-independent.
 Indeed, the binding sites I want to compare are not necessarily related
 in terms of amino-acid composition, but I'd like to still be able to detect
 similarities between them.
 Does anyone have suggestions?
 Thank you.

 Sarah

 --
 Sarah Barelier, Ph.D.
 Postdoctoral Researcher
 Shoichet Lab, UCSF
 sarah.barel...@blur.compbio.ucsf.edu

 Department of Pharmaceutical Chemistry
 1700 4th Street, Byers Hall, Room N501
 San Francisco, CA 94158-2550




 --
 Daisuke




-- 
Sarah Barelier, Ph.D.
Postdoctoral Researcher
Shoichet Lab, UCSF
sarah.barel...@blur.compbio.ucsf.edu

Department of Pharmaceutical Chemistry
1700 4th Street, Byers Hall, Room N501
San Francisco, CA 94158-2550

[ccp4bb] off-topic: binding site comparison

2014-10-31 Thread Sarah Barelier 
Dear all,
I'm sorry, this is a bit off-topic. I'm looking for a tool to compare pairs of 
binding sites.
It doesn't need to be high-throughput, since I'll only be comparing ~100 pairs, 
but I'd like it to be robust and, more importantly, alignment-independent.
Indeed, the binding sites I want to compare are not necessarily related in 
terms of amino-acid composition, but I'd like to still be able to detect 
similarities between them.
Does anyone have suggestions?
Thank you.

Sarah

-- 
Sarah Barelier, Ph.D.
Postdoctoral Researcher
Shoichet Lab, UCSF
sarah.barel...@blur.compbio.ucsf.edu

Department of Pharmaceutical Chemistry
1700 4th Street, Byers Hall, Room N501
San Francisco, CA 94158-2550