[ccp4bb] Secondary structure prediction for billions of sequences ?

Hi all It’s been a while since I posted on this group so apologies for a slightly tangential, non CCP4 question. I wanted to get secondary structure predictions for designing a library of 50-100 amino acid peptides. The library could get very large ( 10^9) and I was wondering if there is a way to

Re: [ccp4bb] secondary structure prediction

Dear Zheng, There are some things you can try, which depend on the computational resources you have available and the time you want to wait. The best would be to try Rosetta ab initio modelling. Preferably, you would run Rosetta using your local installation but if you don’t have Rosetta instal

Re: [ccp4bb] secondary structure prediction

bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Missoury Sophia [sophia.misso...@u-psud.fr] Sent: Wednesday, December 06, 2017 9:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] secondary structure prediction Modeller Sophia Missoury De: "S

Re: [ccp4bb] secondary structure prediction

yes | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月07日 09:11，zheng zhou 写道： Thanks for many advices. I was not clear in the previous email. I know the close homologous protein (20% identity, total 500aa), but the fragment hits (30~40aa, identity 40~50%) are from other p

Re: [ccp4bb] secondary structure prediction

Thanks for many advices. I was not clear in the previous email. I know the close homologous protein (20% identity, total 500aa), but the fragment hits (30~40aa, identity 40~50%) are from other proteins in PDB. I am trying to see whether the fragments from non-homologous proteins may help the second

Re: [ccp4bb] secondary structure prediction

Modeller Sophia Missoury - Mail original - De: "Smith Liu" À: CCP4BB@JISCMAIL.AC.UK Envoyé: Mercredi 6 Décembre 2017 16:04:12 Objet: Re: [ccp4bb] secondary structure prediction Rosetta Smith Liu 邮箱：smith_liu...@163.com 签名由

Re: [ccp4bb] secondary structure prediction

I would try your local bioinformatician (or a remote one if there isn't any one local). With the sequence in the mail, I could have given it a shot... Gert On 12/6/2017 3:14 PM, zheng zhou wrote: Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for stru

Re: [ccp4bb] secondary structure prediction

Dear Zheng, You might want to try the tools at: https://ccd.rhpc.nki.nl Tassos On Dec 6, 2017, at 15:14, zheng zhou mailto:zhengzho...@gmail.com>> wrote: Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for structure studies. It only has a homolog struc

Re: [ccp4bb] secondary structure prediction

Rosetta | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月06日 22:14，zheng zhou 写道： Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for structure studies. It only has a homolog structure in PDB with sequence identity ~20%. When I bla

[ccp4bb] secondary structure prediction

Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for structure studies. It only has a homolog structure in PDB with sequence identity ~20%. When I blast against PDB sequence, there are quite a few motif hits (30~40aa, identity 40~50%). Any prediction tools ut