[ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

Hi, everyone, I want to run plenty secondary structure prediction works and online prediction costs a lot of time. So I expect local software for secondary structure prediction will greatly help to my work. Has anyone ever configed such local secondary structure prediction server? Any suggestio

[ccp4bb] Random coil protein

Dear users, I'm just approaching to a new project...so, I have evidences of an interaction between the N-terminus region of a protein with its own C-terminal domain. The C-terminal domain is perfectly folded (easily expressed and purified), instead of the N-terminal one that is mostly random coi

Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

Hi, I would just submit your sequence to Phyre (http://www.sbg.bio.ic.ac.uk/~phyre/). You'll get, among other good things, the secondary structure predictions, perhaps even a 3-D structure prediction, depending on the similarity of your sequence to that of known structures.   

Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

I highly recommend SABLE if you want to set up your own internal tool. It's pretty easy. http://sable.cchmc.org/ Adamczak, Porollo and Meller, Proteins 56, 2004 SABLE uses a lot of PSI-BLAST runs, so plan your system accordingly. Artem On Sun, Dec 4, 2011 at 6:00 AM, 商元 wrote: > Hi, everyone

Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

You can run psipred yourself locally by downloading the software available here: http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/ You will also require blast and a local sequence database (usually uniref90). Have a look at the README http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README

Re: [ccp4bb] MR problem

Dear Ping, First thing to ask: Do you know with 100% certainty if your crystals contain a complex? If your crystals are large enough (and you have more than one) you can check this on SDS-PAGE or with mass-spec as long as you are sure to remove all surrounding mother liquid that may contamina

Re: [ccp4bb] MR problem

Dear Ping, First thing to ask: Do you know with 100% certainty if your crystals contain a complex? If your crystals are large enough (and you have more than one) you can check this on SDS-PAGE or with mass-spec as long as you are sure to remove all surrounding mother liquid that may contaminate y

[ccp4bb]

http://science.loriz.ca/lipids/includes/templates/imagec.html

[ccp4bb] Job Opportunity - Head of the Berkeley Center for Structural Biology

The Physical Biosciences Division at Lawrence Berkeley National Laboratory is seeking candidates for the Head of the Berkeley Center for Structural Biology. This position provides scientific, technical and operational oversight of the BCSB at the Advanced Light Source (ALS), a third generation s

[ccp4bb] article about Vladimir Vand

I found an article that might interest some of you in a journal that most crystallographers probably do not read: Alena Solcova, Michal Krizek Vladimir Vand (1911-1968): Pioneer of Computational Methods in Crystallography IEEE Annals of the History of Computing, Vol. 33, No. 4 October-December

Re: [ccp4bb] Software for optimizing drug molecules

Dear Jie, There isn't much that is free these days. Openeye offers "free" academic licenses but there is a clause in their agreement that they will claim license fees should the molecule become commercial. Could you be a little bit more specific a about what type of optimization you are after?

[ccp4bb] 回复：Re: [ccp4bb] MR problem

Dear Remy, Thank you for your suggestion. I have confirmed that two protein exit in the crystal. Both of protein are single domain protein. Maybe I will check whether the real solution is rejected by program. Thanks. Ping - 原始邮件 - 发件人：Remy Loris 收件人：CCP4BB@JISCMAIL.AC.UK 主题：Re: [ccp4bb]