Published Paper Details:

Rice Tungro disease poses a significant challenge to rice cultivation throughout Southeast Asia and arises from coinfection by Rice Tungro Bacilliform Virus (RTBV) and Rice Tungro Spherical Virus (RTSV). RTSV plays a critical role in enabling the efficient transmission of RTBV through its insect vector, the green leafhopper (Nephotettix virescens). Among the viral components, the CP3 capsid protein of RTSV is essential for assembling virions and mediating interactions with both the host and the insect vector. In this investigation, we employed a range of bioinformatics tools to carry out an in silico characterization of the CP3 gene. The gene's nucleotide sequence was first translated into its amino acid counterpart, followed by an in-depth analysis of its physicochemical properties, secondary and tertiary structural features, and immunogenic potential. Using AlphaFold predictions and comparative homology modeling, high-confidence three-dimensional structural models were constructed and validated through tools such as Ramachandran plot evaluation, ProSA-web scoring, and Verify3D analysis. The core ?-barrel architecture, which is typical of viral capsid proteins, exposes potential surface epitopes, which may be involved in immune recognition or interactions with the insect vector [12]. Furthermore, docking simulations and electrostatic surface potential analysis were used to pinpoint likely binding interfaces for host or vector proteins. Strong sequence conservation among varied geographical RTSV isolates was discovered by evolutionary analysis, highlighting the possibility of broad-based diagnostic markers and resistance targets. Overall, this study provides detailed structural and functional insights into the RTSV CP3 protein and supports its relevance for applications in diagnostics, rice tungro infection management or pesticide development, and engineered resistance. It also shows how computer modeling can considerably progress plant virology, particularly in the lack of experimental structural evidence.