Anderson A, Weng Z
Department of Biomedical Engineering, Boston University, Massachusetts, USA.
J Mol Graph Model. 1999 Jun-Aug;17(3-4):180-6, 217. doi: 10.1016/s1093-3263(99)00029-7.
We have developed an interactive docking program called VRDD. It offers various modes of displaying molecules in an immersive, three-dimensional virtual reality (VR) environment. It allows a user to interactively perform molecular docking aided by automatic docking and side chain conformational search. Binding free energies are computed in real time, and the program enables the user to explore only clash-free orientations of a ligand. VRDD also supplies visual and auditory feedback during docking and side chain search, indicating the levels of atomic overlap and interaction energy. The stunning VR graphics immerse users in the scene and can maximally stimulate their design intuition. We have tested VRDD on three cases with increasing complexity: a nine-residue-long peptide bound to a major histocompatibility complex (MHC) molecule, barstar bound to barnase, and an antibody bound to a hemagglutinin. Without prior knowledge, combinations of hand-docking and automatic refinement led to accurate complex structures for the first two complexes. The third case, for which all automatic docking algorithms failed to identify the correct complex in a previous blind test, also failed for VRDD. Our results show that the combination of VR docking and automatic docking can make unique contributions to molecular modeling.
我们开发了一个名为VRDD的交互式对接程序。它提供了多种在沉浸式三维虚拟现实（VR）环境中显示分子的模式。它允许用户在自动对接和侧链构象搜索的辅助下交互式地进行分子对接。实时计算结合自由能，并且该程序仅允许用户探索配体无冲突的取向。VRDD在对接和侧链搜索过程中还提供视觉和听觉反馈，指示原子重叠和相互作用能的水平。令人惊叹的VR图形让用户沉浸在场景中，并能最大程度地激发他们的设计直觉。我们在三个复杂度不断增加的案例上测试了VRDD：一个与主要组织相容性复合体（MHC）分子结合的九肽、与核糖核酸酶抑制剂结合的芽孢杆菌RNA酶抑制剂以及与血凝素结合的抗体。在没有先验知识的情况下，手动对接和自动优化的组合为前两个复合物产生了准确的复合物结构。在之前的盲测中所有自动对接算法都未能识别出正确复合物的第三个案例，VRDD也未能成功解决。我们的结果表明，VR对接和自动对接的结合可为分子建模做出独特贡献。
