BACKGROUND The capsid coated protein of Bluetongue virus (BTV) VP2 is responsible for BTV transmission by the Culicoides vector to vertebrate hosts. Besides, VP2 is responsible for BTV entry into permissive cells and hence plays a major role in disease progression. However, its mechanism of action is still unknown. OBJECTIVE The present investigation aimed to predict the 3D structure of Viral Protein 2 of the bluetongue virus assisted by Optimized Potential for Liquid Simulations (OPLS), structure validation, and an active site prediction. METHODS The 3D structure of the VP2 protein was built using a Python-based Computational algorithm. The templates were identified using Smith waterman's Local alignment. The VP2 protein structure validated using PROCHECK. Molecular Dynamics Simulation (MDS) studies were performed using an academic software Desmond, Schrodinger dynamics, for determining the stability of a model protein. The Ligand-Binding site was predicted by structure comparison using homology search and proteinprotein network analysis to reveal their stability and inhibition mechanism, followed by the active site identification. RESULTS The secondary structure of the VP2 reveals that the protein contains 220 alpha helix atoms, 40 310 helix, 151 beta sheets, 134 coils and 424 turns, whereas the 3D structure of Viral Protein 2 of BTV has been found to have 15774 total atoms in the structure. However, 961 amino acids were found in the final model. The dynamical cross-correlation matrix (DCCM) analysis tool identifies putative protein domains and also confirms the stability of the predicted model and their dynamical behavior difference with the correlative fluctuations in motion. CONCLUSION The biological interpretation of the Viral Protein 2 was carried out. DCCM maps were calculated, using a different coordinate reference frame, through which, protein domain boundaries and protein domain residue constituents were identified. The obtained model shows good reliability. Moreover, we anticipated that this research should play a promising role in the identification of novel candidates with the target protein to inhibit their functional significance.

中文翻译：

---

液体模拟（OPLS）最佳电位辅助的蓝舌病毒外壳蛋白VP2的计算机辅助结构预测。

背景技术蓝舌病病毒（BTV）VP2的衣壳包被蛋白负责通过Culicoides载体将BTV传播给脊椎动物宿主。此外，VP2负责BTV进入允许细胞，因此在疾病进展中起主要作用。但是，其作用机理仍然未知。目的本研究旨在通过优化的液体模拟潜力（OPLS），结构验证和活性位点预测来预测蓝舌病毒病毒蛋白2的3D结构。方法使用基于Python的计算算法构建VP2蛋白的3D结构。使用史密斯沃特曼的本地比对来识别模板。VP2蛋白结构已使用PROCHECK进行了验证。使用学术软件Desmond，Schrodinger动力学进行了分子动力学模拟（MDS）研究，以确定模型蛋白的稳定性。配体结合位点通过使用同源搜索和蛋白质网络分析的结构比较来预测，以揭示其稳定性和抑制机制，然后进行活性位点鉴定。结果VP2的二级结构显示该蛋白包含220个α螺旋原子，40310个螺旋，151个β片，134个线圈和424匝，而BTV病毒蛋白2的3D结构已被发现具有15774个总原子。结构。但是，在最终模型中发现了961个氨基酸。动态互相关矩阵（DCCM）分析工具可以识别推定的蛋白质结构域，还可以确定预测模型的稳定性及其与运动相关波动的动态行为差异。结论进行了病毒蛋白2的生物学解释。使用不同的坐标参考系计算DCCM图，通过该图可识别蛋白质结构域边界和蛋白质结构域残基成分。所获得的模型显示出良好的可靠性。此外，我们预计这项研究将在鉴定具有目标蛋白的新候选物方面发挥有希望的作用，以抑制其功能重要性。结论进行了病毒蛋白2的生物学解释。使用不同的坐标参考系计算DCCM图，通过该图可识别蛋白质结构域边界和蛋白质结构域残基组成。所获得的模型显示出良好的可靠性。此外，我们预计这项研究应在鉴定具有目标蛋白的新候选物方面发挥有希望的作用，以抑制其功能重要性。结论进行了病毒蛋白2的生物学解释。使用不同的坐标参考系计算DCCM图，通过该图可识别蛋白质结构域边界和蛋白质结构域残基组成。所获得的模型显示出良好的可靠性。此外，我们预计这项研究应在鉴定具有目标蛋白的新候选物方面发挥有希望的作用，以抑制其功能重要性。