VRDD: Applying virtual reality visualization to protein docking and design
VRDD: Applying virtual reality visualization to protein docking and design
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DOI：
10.1016/s1093-3263(99)00029-7
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发表时间：
1999-06-01
影响因子：
2.9
通讯作者：
Weng, ZP
中科院分区：
文献类型：
--
作者：
Anderson, A;Weng, ZP
我们开发了一个交互式对接程序VRDD。它提供了在沉浸式三维虚拟现实（VR）环境中显示分子的各种模式。它允许用户通过自动对接和侧链构象搜索交互式地进行分子对接。结合自由能计算在真实的时间，该计划使用户能够探索只有无冲突的配体取向。VRDD还在对接和侧链搜索期间提供视觉和听觉反馈，指示原子重叠和相互作用能量的水平。令人惊叹的VR图形让用户沉浸在场景中，可以最大限度地激发他们的设计直觉。我们已经测试了VRDD的三个案件日益复杂：一个九个残基长的肽结合到一个主要组织相容性复合体（MHC）分子，芽孢杆菌RNA酶结合，和抗体结合到血凝素。在没有先验知识的情况下，手动对接和自动细化的组合导致了前两个复合物的精确复杂结构。第三种情况下，所有自动对接算法未能在先前的盲测中识别出正确的复合物，VRDD也失败了。我们的研究结果表明，VR对接和自动对接的结合可以为分子建模做出独特的贡献。(C)2000年，Elsevier Science Inc.
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. (C) 2000 by Elsevier Science Inc.