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Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

https://doi.org/10.1371/journal.pcbi.1006842

Bliven, Spencer E. ; Lafita, Aleix ; Rose, Peter W. ; Capitani, Guido ; Prlić, Andreas ; Bourne, Philip E. ; Darling, Aaron E. ( April 2019 , PLOS Computational Biology)

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BioJava 5: A community driven open-source bioinformatics library

https://doi.org/10.1371/journal.pcbi.1006791

Lafita, Aleix ; Bliven, Spencer ; Prlić, Andreas ; Guzenko, Dmytro ; Rose, Peter W. ; Bradley, Anthony ; Pavan, Paolo ; Myers-Turnbull, Douglas ; Valasatava, Yana ; Heuer, Michael ; et al ( February 2019 , PLOS Computational Biology)

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Assessment of protein assembly prediction in CASP13

https://doi.org/10.1002/prot.25795

Guzenko, Dmytro ; Lafita, Aleix ; Monastyrskyy, Bohdan ; Kryshtafovych, Andriy ; Duarte, Jose M. ( August 2019 , Proteins: Structure, Function, and Bioinformatics)

Abstract
We present the assembly category assessment in the 13th edition of the CASP community‐wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions, we observe that ignoring the oligomeric state of the targets hinders modeling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modeling. Homology modeling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should see more integrated approaches where subunits are modeled in the context of the assemblies they form.

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