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PconsFam: An Interactive Database of Structure Predictions of Pfam Families
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).ORCID iD: 0000-0003-3534-2986
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Number of Authors: 62019 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 431, no 13, p. 2442-2448Article in journal (Refereed) Published
Abstract [en]

At present, about half of the protein domain families lack a structural representative. However, in the last decade, predicting contact maps and using these to model the tertiary structure for these protein families have become an alternative approach to gain structural insight. At present, reliable models for several hundreds of protein families have been created using this approach. To increase the use of this approach, we present PconsFam, which is an intuitive and interactive database for predicted contact maps and tertiary structure models of the entire Pfam database. By modeling all possible families, both with and without a representative structure, using the PconsFold2 pipeline, and running quality assessment estimator on the models, we predict an estimation for how confident the contact maps and structures are for each family.

Place, publisher, year, edition, pages
2019. Vol. 431, no 13, p. 2442-2448
Keywords [en]
contact maps, structure prediction, folding pipeline, Pfam
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-172037DOI: 10.1016/j.jmb.2019.01.047ISI: 000474675300006PubMedID: 30796988OAI: oai:DiVA.org:su-172037DiVA, id: diva2:1346198
Available from: 2019-08-27 Created: 2019-08-27 Last updated: 2020-01-23Bibliographically approved

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Lamb, JohnJarmolinska, AleksandraMichel, MircoMenéndez-Hurtado, DavidElofsson, Arne
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