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Background:  The endoplasmic reticulum (ER) is an important organelle in eukaryotic cells. It is involved in many important biological processes, such as cell metabolism, protein synthesis, and post-translational modification. The proteins that reside within the ER are called ER-resident proteins. These proteins are closely related to the biological functions of the ER. The difference between the ER-resident proteins and other non-resident proteins should be carefully studied.    Methods:  We developed a support vector machine (SVM)-based method. We developed a U-shaped weight-transfer function and used it, along with the positional-specific physiochemical properties (PSPCP), to integrate together sequence order information, signaling peptides information, and evolutionary information.    Result:  Our method achieved over 86% accuracy in a jackknife test. We also achieved roughly 86% sensitivity and 67% specificity in an independent dataset test. Our method is capable of identifying ER-resident proteins.

Predicting Endoplasmic Reticulum Resident Proteins Using Auto-Cross Covariance Transformation With a U-Shaped Residue Weight-Transfer Function