Chen, Xue-wenJeong, Jong CheolDermyer, Patrick2014-04-152014-04-152010-09-30Chen, Xue-wen, Jong Cheol Jeong, and Patrick Dermyer. 2011. “KUPS: Constructing Datasets of Interacting and Non-Interacting Protein Pairs with Associated Attributions.” Nucleic Acids Research 39 (Database issue): D750–D754. http://dx.doi.org/10.1093/nar/gkq943https://hdl.handle.net/1808/13489KUPS (The University of Kansas Proteomics Service) provides high-quality protein–protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets. Each data set is built from the overall database, which includes 185 446 IPPs and ∼1.5 billion NIPs from five primary databases: IntAct, HPRD, MINT, UniProt and the Gene Ontology. The IPP set can be set to specific model organisms, interaction types and experimental evidence. The NIP set can be generated using four different strategies, which can alleviate biased estimation problems. Lastly, multiple features can be provided for all of the IPP and NIP pairs. Additionally, KUPS provides two benchmark data sets to help researchers compare their algorithms to existing approaches. KUPS is freely available at http://www.ittc.ku.edu/chenlab.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by-nc/2.5Article10.1093/nar/gkq943https://orcid.org/0000-0002-5024-2927openAccess