The beta-sheet is an element of protein secondary structure, and intra-/intermolecular beta-sheet interactions play pivotal roles in biological regulatory processes including scaffolding, transporting, and oligomerization. In nature, a beta-sheet formation is tightly regulated because dysregulated beta-stacking often leads to severe diseases such as Alzheimer's, Parkinson's, systemic amyloidosis, or diabetes. Thus, the identification of intrinsic beta-sheet-forming propensities can provide valuable insight into protein designs for the development of novel therapeutics. However, structure-based design methods may not be generally applicable to such amyloidogenic peptides mainly owing to high structural plasticity and complexity. Therefore, an alternative design strategy based on complementary sequence information is of significant importance. Herein, we developed a database search method called beta-Stacking Interaction DEsign for Reciprocity (B-SIDER) for the design of complementary beta-strands. This method makes use of the structural database information and generates target-specific score matrices. The discriminatory power of the B-SIDER score function was tested on representative amyloidogenic peptide substructures against a sequence-based score matrix (PASTA 2.0) and two popular ab initio protein design score functions (Rosetta and FoldX). B-SIDER is able to distinguish wild-type amyloidogenic beta-strands as favored interactions in a more consistent manner than other methods. B-SIDER was prospectively applied to the design of complementary beta-strands for a splitGFP scaffold. Three variants were identified to have stronger interactions than the original sequence selected through a directed evolution, emitting higher fluorescence intensities. Our results indicate that B-SIDER can be applicable to the design of other beta-strands, assisting in the development of therapeutics against disease-related amyloidogenic peptides.