The structural model of begomovirus AC1 protein is useful for understanding biological function at molecular level and docking study. For this study we have used the ProSA program (Protein Structure Analysis) tool to establish the structure prediction and modeling of protein. This tool was used for refinement and validation of experimental protein structures. Potential problems of protein structures based on energy plots are easily seen by ProSA and are displayed in a three-dimensional manner. In the present study we have selected different AC1 proteins of begomovirus strains (YP_003288785, YP_002004579, and YP_003288773) for structural analysis and display of energy plots that highlight potential problems spotted in protein structures. The 3D models of Rep proteins with recognized errors can be effectively used for in silico docking study for development of potential ligand molecules against begomovirus infection. 1. Introduction Geminiviruses were recognized in 1978 by the International Committee on the Taxonomy of viruses on the basis of their unique virion morphology and possession of ssDNA as their genomic material [1, 2]. Geminiviridae is one of the largest plant virus family; its members have a circular, single-stranded DNA (ssDNA) genome of approximately 2.7–5.2？kb encapsulated within twinned (geminate) icosahedral virions. The protein coat of geminiviridae consists of one type protein molecule of about 28？kd molecular weight. Based on their genome arrangement and biological properties, geminiviruses are classified into one of four genera: Mastrevirus, Curtovirus, Topocuvirus, and Begomovirus [3]. Begomoviruses, currently hold 200 species [4] and contain dicotyledonous infecting whitefly transmitted viruses in the family Geminiviridae, have either bipartite genomes (DNA-A and DNA-B) or monopartite genomes resembling DNA-A. DNA-A typically has six open reading frames (ORFs): AV1/V1 (coat protein, CP) and AV2/V2 (AV2/V2 protein) on the virion-sense strand and AC1/C1 (replication initiation protein, Rep), AC2/C2 (transcriptional activator, TrAP), AC3/C3 (replication enhancer, REn), and AC4/C4 (AC4/C4 protein) on the complementary-sense strand. DNA-B has two ORFs, encoding movement proteins: BV1 (nuclear shuttle protein, NSP) on the virus-sense strand and BC1 (movement protein, MP) on the complementary-sense strand [5]. Computational methods can be applied for the prediction of unknown structures of experimental and theoretical models of virus proteins [6, 7], but the problem in structural biology is the recognition of errors in experimental and
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