Genetic code refers to a set of rules that assign trinucleotides called codons to amino acids in the process of protein synthesis. Investigating the genetic code's logic and its evolutionary origin has always been both intriguing and challenging. While the correspondence rules between codons and amino acids in the genetic code are well-known, it is still unclear whether those assignments can be explained based on energetic or/and entropic arguments. As an attempt at deciphering basic thermodynamic rules governing DNA translation, we used molecular docking to investigate the ability of amino acids to bind to their corresponding anticodon compared to other codons. The total number of 1280 direct docking interactions have been performed for each amino acid-codon/anti-codon case to find whether the amino acids have a preference to bind to their cognate anticodons or codons. Based on docking scores which are expected to correlate with binding affinity, no correlation with genetic correspondence rules was observed suggesting a more subtle process, other than direct binding, to explain codon-amino-acid specificity.

遗传密码是指在蛋白质合成过程中将称为密码子的三核苷酸分配给氨基酸的一组规则。研究遗传密码的逻辑及其进化起源一直既有趣又具有挑战性。虽然遗传密码中密码子和氨基酸之间的对应规则是众所周知的，但仍不清楚这些分配是否可以基于能量或/和熵参数来解释。作为破译控制 DNA 翻译的基本热力学规则的尝试，我们使用分子对接来研究与其他密码子相比氨基酸与其相应反密码子结合的能力。对每个氨基酸-密码子/反密码子情况进行了 1280 次直接对接相互作用的总数，以确定氨基酸是否具有与其同源反密码子或密码子结合的偏好。基于预计与结合亲和力相关的对接评分，没有观察到与遗传对应规则的相关性，这表明除了直接结合之外，还有一个更微妙的过程来解释密码子 - 氨基酸 - 氨基酸的特异性。