Computational tools for the prediction of protein orientations on material surfac

描述（由申请人提供）：了解蛋白质在材料表面的取向对于生物技术中应用的材料表面设计至关重要。然而，在原子水平上确定蛋白质的取向仍然是一个挑战。各种表面分析技术，如飞行二次离子质谱法、和频产生振动谱法和近边缘x射线吸收精细结构，已经发展到探测蛋白质吸附在表面的取向。然而，这种实验产生的光谱可能非常复杂，如果没有合适的后处理软件，推断结果可能很困难。在这个项目中，开发了软件工具，利用蛋白质的可用三维结构来预测在给定表面上蛋白质的特定方向的情况下要测量的光谱。此外，将建立一个可公开访问的在线服务器，该服务器将使用蒙特卡罗模拟来预测用户在选定表面上上传的蛋白质的方向。蒙特卡罗搜索可以通过包括可用的实验数据来指导，以便改进实验提出的模型，或者在不同技术提出矛盾模型时区分最可能的方向。如果没有实验数据，服务器将提供蛋白质取向的估计值，该估计值可用于生成假设或作为更复杂的蛋白质表面相互作用计算的起始构象。

DESCRIPTION (provided by applicant): Understanding the orientation of proteins on material surfaces is of crucial importance for the design of material surfaces with applications in biotechnology. However, the determination of protein orientation at atomic level of detail remains a challenge. Various surface analysis techniques, like flight secondary ion mass spectrometry, sum frequency generation vibrational spectrometry and near-edge X-ray absorption fine structure, have been developed to probe the orientation of proteins adsorbed onto surfaces. However, the spectra generated by this type of experiments can be very complex and extrapolating a result can be difficult if not impossible without suitable post-processing software. In this project, software tools are developed which make use of available three-dimensional structures of proteins to predict the spectrum that would be measured given a particular orientation of the protein on a surface. Furthermore, a publicly accessible online server will be setup which, using Monte Carlo simulations, will predict the orientation of a protei uploaded by a user on a selected surface. The Monte Carlo search can be guided by including available experimental data in order to refine a model suggested by the experiments or discriminate the most likely orientation when contradicting models are suggested by different techniques. If no experimental data is present, the server will provide an estimate of the protein orientation that can be either used to generate hypotheses or as the starting conformation for more complex calculations of the protein-surface interaction.