Protein domains are subunits that can fold and evolve independently. The identification of protein domains is essential for protein structure determination and functional annotations. ThreaDom2 and DomEx3 are two methods recently developed for protein domain boundary recognition and especially discontinuous domain prediction. ThreaDomEx combines ThreaDom and DomEx into a unified on-line server system for more accurate and user-friendly domain predictions on sequences of both continuous and discontinuous domain structures. ThreaDomEx takes the amino acid sequence of the query protein as input. It first creates multiple threading alignments to recognize homologous and analogous template structures, from which a domain conservation score is then calculated for deducing the domain boundaries. Next, a boundary clustering method is used to optimize the domain model selections. For discontinuous domain structures, a symmetric alignment algorithm is applied to further integrate and refine the domain assignments. Output of the server consists of: (a) the predicted domain boundaries and discontinuous domains; (b) the visualized distribution of domain conserve score, predicted secondary structure and solvent accessiblity; (c) the threading templates used by ThreaDomEx. The server allows users to interactively edit, save, or re-detect the domain models of the proteins.
For each target, the output data are kept online for three months before they are removed from the server.
1. Yan wang, Jian Wang, Qiang Shi, Ruiming Li，Zhidong Xue, Yang Zhang. ThreaDomEx: A unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. Nucleic Acids Research, doi:10.1093/nar/gkx410(2017).
2. Z Xue, D Xu, Y Wang, Y Zhang. ThreaDom: Extracting Protein Domain Boundary Information from Multiple Threading Alignments. Bioinformatics, 29: i247-i256 (2013).
3. Zhidong Xue, Richard Jang, Brandon Govindarajoo, Yichu Huang, Yan Wang. Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains. PLoS ONE 10(10): e0141541. doi:10.1371/journal. pone.0141541 (2015).