HelixHelix

HelixHelix is a bioinformatics platform designed for the analysis and visualization of nucleic‑acid and protein secondary‑structure motifs. First released in 2018 by a consortium of computational biologists at the Institute for Molecular Modeling, the software integrates algorithms for double‑helix detection, helix‑helix interaction mapping, and comparative structural alignment.

The core of HelixHelix consists of a hybrid pipeline that combines sequence‑based prediction, using hidden Markov models, with three‑dimensional geometry assessment derived from cryo‑EM and X‑ray crystallography data. Users can import raw sequence files, PDB structures, or electron density maps, after which the program identifies canonical α‑helices, β‑sheets, and coiled‑coil regions, and further detects paired helices that form superhelical assemblies. The output includes interactive graphics, quantitative scores for helix stability, and a database‑compatible annotation file.

Since its introduction, HelixHelix has been employed in studies of transcription factors, membrane proteins, and viral capsids, where helix‑helix packing influences functional conformation. Publications have cited the tool for improving the accuracy of homology models by up to 12 % compared with conventional methods. In 2021 a cloud‑based version was launched, allowing collaborative annotation and integration with genome‑wide association pipelines.

HelixHelix is distributed under an open‑source license, with source code hosted on a public repository and regular updates that incorporate machine‑learning refinements. Ongoing development aims to expand support for RNA triple‑helix motifs and to provide automated reporting for high‑throughput structural genomics projects.