Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
2013 (English)In: Proteins: Structure, Function, and Genetics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 81, no 11, 1980-1987 p.Article in journal (Refereed) Published
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies. Proteins 2013; 81:1980-1987.
Place, publisher, year, edition, pages
2013. Vol. 81, no 11, 1980-1987 p.
CAPRI, hemagglutinin, binding, deep mutational scanning, yeast display
Medical and Health Sciences
IdentifiersURN: urn:nbn:se:uu:diva-211018DOI: 10.1002/prot.24356ISI: 000325980300011OAI: oai:DiVA.org:uu-211018DiVA: diva2:665483