Large-scale structure prediction by improved contact predictions and model quality assessment

Michel, MircoStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab) (författare)

Motivation: Accurate contact predictions can be used for predicting the structure of proteins. Until recently these methods were limited to very big protein families, decreasing their utility. However, recent progress by combining direct coupling analysis with machine learning methods has made it possible to predict accurate contact maps for smaller families. To what extent these predictions can be used to produce accurate models of the families is not known. Results: We present the PconsFold2 pipeline that uses contact predictions from PconsC3, the CONFOLD folding algorithm and model quality estimations to predict the structure of a protein. We show that the model quality estimation significantly increases the number of models that reliably can be identified. Finally, we apply PconsFold2 to 6379 Pfam families of unknown structure and find that PconsFold2 can, with an estimated 90% specificity, predict the structure of up to 558 Pfam families of unknown structure. Out of these 415 have not been reported before. Availability: Datasets as well as models of all the 558 Pfam families are available at http://c3.pcons.net. All programs used here are freely available.

Menéndez Hurtado, DavidStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)(Swepub:su)dmene (författare)
Uziela, KarolisStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)(Swepub:su)kuzie (författare)
Elofsson, ArneStockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)(Swepub:su)aelof (författare)
Stockholms universitetInstitutionen för biokemi och biofysik (creator_code:org_t)

Ingår i:Bioinformatics: Oxford University Press (OUP)33:14, s. 123-1291367-48031367-48111460-2059

Av författaren/redakt...: Michel, Mirco; Menéndez Hurtado ...; Uziela, Karolis; Elofsson, Arne

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