[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 predict the secondary structure for this large set of sequences that scales well. I am currently using psipred which works well, but runs one sequences at a time and generates the desired prediction with concurrent creation of many temp files. Although I realize this is solvable with the current approach, by parallelizing the calls I was wondering if there are other approaches that are suitable for this. Thanks for your help in advance Hari Jayaram To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
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 installed, this can be annoying to do. You can also use the Rosie web server (the Rosetta web server), but it takes long time to compute. Other faster solutions for "ab initio" modelling would be Quark (in case your protein is short), I-tasser or RaptorX Contact Prediction web servers. I am very happy with the latter, I use it frequently when I don’t want to wait for Rosetta. You can also try homology modelling, but this would be less reliable when the few motifs you find do not overlap and do not cover the entire protein. Anyway, for homology modelling you can try , for example, Modeller after HHPred (you can do this using the MPI Bioinformatics toolkit) or RaptorX Structure Prediction. I hope this helps you. Best regards and good luck! Dr. Joana Pereira -- Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Spemannstraße 35 72076 Tübingen GERMANY > On 06 Dec 2017, at 15:14, zheng zhou wrote: > > 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 utilize this information? > > Thanks for your advice in advance. > > Best, > > Zheng
Re: [ccp4bb] secondary structure prediction
I'm fond of RaptorX ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu<mailto:pr...@uchicago.edu> https://voices.uchicago.edu/phoebericelab/ From: CCP4 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: "Smith Liu" À: CCP4BB@JISCMAIL.AC.UK Envoyé: Mercredi 6 Décembre 2017 16:04:12 Objet: Re: [ccp4bb] secondary structure prediction Rosetta <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?iconUrl=https://nos.netease.com/mail-online/qiyelogo/defaultAvatar.png&name=Smith%20Liu&uid=smith_liu123%40163.com&ftlId=1&items=%5B%22%E9%82%AE%E7%AE%B1%EF%BC%9Asmith_liu123%40163.com%22%5D> [https://nos.netease.com/mail-online/qiyelogo/defaultAvatar.png] Smith Liu 邮箱：smith_liu...@163.com 签名由 网易邮箱大师<https://mail.163.com/dashi/dlpro.html?from=mail88> 定制 在2017年12月06日 22:14，zheng zhou<mailto:zhengzho...@gmail.com> 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 blast against PDB sequence, there are quite a few motif hits (30~40aa, identity 40~50%). Any prediction tools utilize this information? Thanks for your advice in advance. Best, Zheng
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 proteins in PDB. I am trying to see whether the fragments from non-homologous proteins may help the secondary structure prediction. Best, Z On Wed, Dec 6, 2017 at 10:14 PM, zheng zhou wrote: > 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 utilize this information? > > Thanks for your advice in advance. > > Best, > > Zheng
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 secondary structure prediction. Best, Z On Wed, Dec 6, 2017 at 10:14 PM, zheng zhou wrote: > 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 utilize this information? > > Thanks for your advice in advance. > > Best, > > Zheng
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 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 blast against PDB sequence, there are quite a few motif hits (30~40aa, identity 40~50%). Any prediction tools utilize this information? Thanks for your advice in advance. Best, Zheng
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 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 utilize this information? Thanks for your advice in advance. Best, Zheng Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
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 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 utilize this information? Thanks for your advice in advance. Best, Zheng
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 blast against PDB sequence, there are quite a few motif hits (30~40aa, identity 40~50%). Any prediction tools utilize this information? Thanks for your advice in advance. Best, Zheng
[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 utilize this information? Thanks for your advice in advance. Best, Zheng
