Effective labeling of molecular surface points for cavity detection and location of putative binding sites.

Mary Ellen Bock, Claudio Garutti, Conettina Guerra
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Abstract

We present a method for detecting and comparing cavities on protein surfaces that is useful for protein binding site recognition. The method is based on a representation of the protein structures by a collection of spin-images and their associated spin-image profiles. Results of the cavity detection procedure are presented for a large set of non-redundant proteins and compared with SURFNET-ConSurf. Our comparison method is used to find a surface region in one cavity of a protein that is geometrically similar to a surface region in the cavity of another protein. Such a finding would be an indication that the two regions likely bind to the same ligand. Our overall approach for cavity detection and comparison is benchmarked on several pairs of known complexes, obtaining a good coverage of the atoms of the binding sites.

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有效标记分子表面点,用于空腔检测和推定结合位点的定位。
我们提出了一种检测和比较蛋白质表面空腔的方法,这对蛋白质结合位点识别很有用。该方法基于一组自旋图像及其相关的自旋图像轮廓来表示蛋白质结构。对大量非冗余蛋白进行了空腔检测,并与SURFNET-ConSurf进行了比较。我们的比较方法是用来找到一个表面区域在一个空腔的蛋白质,是几何上相似的表面区域在另一个蛋白质的空腔。这一发现表明,这两个区域可能与同一配体结合。我们对空腔检测和比较的总体方法以几对已知配合物为基准,获得了结合位点原子的良好覆盖。
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