Proteins are commonly used as molecular targets against pathogens such as viruses and bacteria. However, pathogens can evolve rapidly permitting their populations to increase in protein diversity over time and thus escape to the activity of a molecular therapy. Subsequently, in order to design more durable and robust therapies as well as to understand viral evolution in a host and subsequent transmission, it is central to understand the evolution of pathogen proteins. This understanding can enable the detection of protein regions that can be potential targets for therapies and predict the emergence of molecular resistance against therapies. In this direction, two articles published recently in the Journal of Molecular Evolution investigated the evolution of proteomes of diverse flaviviruses, including Zika virus, Dengue virus and West Nile virus. Here I discuss the importance of considering the evolution of viral proteins, with the use of as realistic as possible models and methods that mimic protein evolution, to improve the design of antiviral therapies.

蛋白质通常用作对抗病原体（例如病毒和细菌）的分子靶标。然而，病原体可以迅速进化，允许它们的种群随着时间的推移增加蛋白质多样性，从而逃避分子治疗的活动。随后，为了设计更持久和稳健的疗法以及了解宿主中的病毒进化和随后的传播，了解病原体蛋白质的进化至关重要。这种理解可以检测蛋白质区域，这些区域可以成为治疗的潜在目标，并预测针对治疗的分子耐药性的出现。在这个方向上，最近发表在Journal of Molecular Evolution上的两篇文章研究了多种黄病毒的蛋白质组进化，包括寨卡病毒、登革热病毒和西尼罗河病毒。在这里，我讨论了考虑病毒蛋白质进化的重要性，并使用尽可能逼真的模型和方法来模拟蛋白质进化，以改进抗病毒疗法的设计。