Re: [ccp4bb] Buried surface area calculation..

[gajanan_pbi...@diat.ac.in] Envoyé : mardi 1 juillet 2014 20:49 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Buried surface area calculation.. Hello, Am working with some DNA binding proteins. If I want to calculate the buried surface area, which software tools should i use? Suggest me some windows based

Re: [ccp4bb] Buried surface area calculation..

Dear Gajanan, areaimol analyses the solvent accessible areas. It is part of ccp4, so it comes with a window. Best, Tim On Wed, Jul 02, 2014 at 12:19:50AM +0530, Gajanan Arbade wrote: > Hello, > > Am working with some DNA binding proteins. If I want to calculate the buried > surface area, whic

[ccp4bb] Buried surface area calculation..

Hello, Am working with some DNA binding proteins. If I want to calculate the buried surface area, which software tools should i use? Suggest me some windows based programs to solve my purpose. Thank you & Regards, Gajanan __ Gajanan K Arbade Research

Re: [ccp4bb] buried surface area

On Wed, 2011-10-19 at 20:17 +0100, Jyotica Batra wrote: > Dear users, > > Are there any programs to calculate percentage of buried surface area that is > polar vs nonpolar? > > Thanks in advance > > Thanks! > Jyotica Surface Racer includes breakdown by atom type (polar vs nonpolar) in the outp

[ccp4bb] buried surface area

Dear users, Are there any programs to calculate percentage of buried surface area that is polar vs nonpolar? Thanks in advance Thanks! Jyotica

Re: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface-summary

Subject: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to sup

Re: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface

Hi, have a look at this paper. I believe it's exactly what you're looking for. Protein-protein interaction and quaternary structure. Janin J, Bahadur RP, Chakrabarti P. Q Rev Biophys. 2008 May;41(2):133-80. Review.PMID: 18812015 http://www.ncbi.nl

Re: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface

Hi, just a place I would perhaps start looking: http://www.ebi.ac.uk/msd-srv/prot_int/picite.html ~L~ __ Lari Lehtiö Pharmaceutical Sciences, Department of Biosciences Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 ht

[ccp4bb] Buried surface area (BSA) vs. oligomeric interface

Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to support this strong interface formation. I am looking for some literature whic

[ccp4bb] Buried surface area (BSA) vs. oligomeric interface

Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to support this strong interface formation. I am looking for some literature whic

[ccp4bb] Buried Surface Area using AreaIMol?

Hello, I'm quite a newbie in using CCP4, so I was wondering if there's anyone kind enough to guide me how to use AreaIMol to get the buried surface area? Apparently, the information I'm getting is the total area and contact area of the chains, which I presume none of the two is pointing o

[ccp4bb] Buried Surface Area - summary

Here was the query.What is the easiest way, these days, to calculate the buried surface area between two subunits of a protein? Here are the software and links received (thank you all):1. 4+ votes for PISA  - This following website is great and does a very nice job of analyzing protein interfaces (

Re: [ccp4bb] buried surface area

I use PISA - it tells you lots of things and I think will do this as well http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html You can download your coordinates.. Will need to name subunits A and B or something I think.. Eleanor Gloria Borgstahl wrote: Hello all, What is the easiest way, th

Re: [ccp4bb] buried surface area

>What is the easiest way, these days, to calculate the buried surface area >between two subunits of a protein? >Thanks, and Happy Friday, Gloria The PISA server from EBI does a nice job: fast overview, but also details if necessary. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html greeting

Re: [ccp4bb] buried surface area

Dear *Gloria* In CNS, you can do it use buried_suface.inp. On 4/28/07, Gloria Borgstahl <[EMAIL PROTECTED]> wrote: Hello all, What is the easiest way, these days, to calculate the buried surface area between two subunits of a protein? Thanks, and Happy Friday, Gloria *

[ccp4bb] buried surface area

Hello all, What is the easiest way, these days, to calculate the buried surface area between two subunits of a protein? Thanks, and Happy Friday, Gloria**Gloria BorgstahlEppley In