Player Exploration Patterns in Interactive Molecular Docking with Electrostatic Visual Cues
Player Exploration Patterns in Interactive Molecular Docking with Electrostatic Visual Cues
复制标题
具有静电视觉提示的交互式分子对接中的玩家探索模式
DOI：
10.1145/3623264.3624463
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Jacobson, Bruna
中科院分区：
文献类型：
--
作者：
Liu, Lin;Adamson, Torin;Tapia, Lydia;Jacobson, Bruna
严肃游戏依赖于感兴趣系统的感官线索来指导玩家执行特定任务。例如，在研究和教育中使用的一个严肃的游戏是交互式分子对接，玩家试图将小分子（配体）与蛋白质（受体）结合，探索可能的分子构象的高维空间。玩家通过一个分数来指导，该分数取决于两个分子相互吸引或排斥的强度，并通过对三维蛋白质表面的视觉检查来寻找配体可能适合的空腔。此外，一些交互式分子对接游戏还可以根据分子表面的电荷分布来显示分子，其中带正电和带负电的区域以不同的颜色显示。假设这种配色方案有助于玩家，因为电荷的吸引和排斥有助于分子之间的静电能，从而得分。在本文中，我们测试是否添加电荷信息作为视觉提示有助于更高的分数和探索更有利的能量状态。对于两组不同的配体-受体对，为了验证我们的假设，我们比较了两个模型：一个模型中玩家没有静电信息，另一个模型中显示静电颜色，玩家被告知根据颜色匹配可能相互吸引的分子部分。我们收集玩家数据并将能量值聚类到状态中，这些状态被视为马尔可夫状态。状态之间的转换被解释为玩家对分子的分数和位置进行重大改变，观察到不同的转换概率对应于两个模型之间的不同探索模式。
Serious games rely on sensory cues from the system of interest to guide players in performing a specific task. For instance, a serious game used in research and education is interactive molecular docking, where players try to bind a small molecule (ligand) to a protein (receptor) exploring the high-dimensional space of possible molecular conformations. Players are guided by a score that depends on how strongly the two molecules attract or repel each other, and by visual inspection of the three-dimensional protein surface in search of cavities where the ligand may fit. In addition, some interactive molecular docking games can also display molecules according to the charge distribution on their surface, where positively and negatively charged regions are shown in different colors. It is assumed that this color scheme helps players, since attraction and repulsion of charges contribute to the electrostatic energy between the molecules, and thus the score. In this paper we test whether adding charge information as a visual cue contributes to higher scores and exploration of more favorable energy states. For two distinct sets of ligand-receptor pairs, to test our hypothesis we compare two models: One in which players have no electrostatic information, and the other where electrostatic colors are displayed, and players are told to match parts of the molecules that may attract each other based on their colors. We collect player data and cluster energy values into states, which are treated as Markov states. Transitions between states are interpreted as players making significant changes to the score and position of the molecules, with observation of different transition probabilities corresponding to distinct exploration patterns between the two models.
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