A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence.
BACKGROUND
Predicting protein interactions involving peptide recognition domains is essential for understanding the many important biological processes they mediate. It is important to consider the binding strength of these interactions to help us construct more biologically relevant protein interaction networks that consider cellular context and competition between potential binders.


RESULTS
We developed a novel regression framework that considers both positive (quantitative) and negative (qualitative) interaction data available for mouse PDZ domains to quantitatively predict interactions between PDZ domains, a large peptide recognition domain family, and their peptide ligands using primary sequence information. First, we show that it is possible to learn from existing quantitative and negative interaction data to infer the relative binding strength of interactions involving previously unseen PDZ domains and/or peptides given their primary sequence. Performance was measured using cross-validated hold out testing and testing with previously unseen PDZ domain-peptide interactions. Second, we find that incorporating negative data improves quantitative interaction prediction. Third, we show that sequence similarity is an important prediction performance determinant, which suggests that experimentally collecting additional quantitative interaction data for underrepresented PDZ domain subfamilies will improve prediction.


METHODS
The Matlab code for our SemiSVR predictor and all data used here are available at http://baderlab.org/Data/PDZAffinity.
Department of Applied Mathematics, College of Science, China Agricultural University, Beijing, 100083, China.
Xiaojian
X
Shao
Chris S H
CS
Tan
Courtney
C
Voss
Shawn S C
SS
Li
Naiyang
N
Deng
Gary D
GD
Bader
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D008024:Ligands; D051379:Mice; D008958:Models, Molecular; D009154:Mutation; D054731:PDZ Domains; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012044:Regression Analysis; D015203:Reproducibility of Results
D008024:Ligands; D010455:Peptides; D011506:Proteins