Motivation The knowledge of potentially druggable binding sites on proteins is an important preliminary step toward the discovery of novel drugs. The computational prediction of such areas can be boosted by following the recent major advances in the deep learning field and by exploiting the increasing availability of proper data. Results In this article, a novel computational method for the prediction of potential binding sites is proposed, called DeepSurf. DeepSurf combines a surface-based representation, where a number of 3D voxelized grids are placed on the protein’s surface, with state-of-the-art deep learning architectures. After being trained on the large database of scPDB, DeepSurf demonstrates superior results on three diverse testing datasets, by surpassing all its main deep learning-based competitors, while attaining competitive performance to a set of traditional non-data-driven approaches. Availability and implementation The source code of the method along with trained models are freely available at https://github.com/stemylonas/DeepSurf.git. Supplementary information Supplementary data are available at Bioinformatics online.

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This paper presents a unified framework for 3D shape retrieval. The method supports multimodal queries (2D images, sketches, 3D objects) by introducing a novel view-based approach able to handle the different types of multimedia data. More specifically, a set of 2D images (multi-views) are automatically generated from a 3D object, by taking views from uniformly distributed viewpoints. For each image, a set of 2D rotation-invariant shape descriptors is produced. The global shape similarity between two 3D models is achieved by applying a novel matching scheme, which effectively combines the information extracted from the multi-view representation. The experimental results prove that the proposed method demonstrates superior performance over other well-known state-of-the-art approaches.

In this paper, a 3D shape-based approach is presented for the efficient search, retrieval, and classification of protein molecules. The method relies primarily on the geometric 3D structure of the proteins, which is produced from the corresponding PDB files and secondarily on their primary and secondary structure. After proper positioning of the 3D structures, in terms of translation and scaling, the Spherical Trace Transform is applied to them so as to produce geometry-based descriptor vectors, which are completely rotation invariant and perfectly describe their 3D shape. Additionally, characteristic attributes of the primary and secondary structure of the protein molecules are extracted, forming attribute-based descriptor vectors. The descriptor vectors are weighted and an integrated descriptor vector is produced. Three classification methods are tested. A part of the FSSP/DALI database, which provides a structural classification of the proteins, is used as the ground truth in order to evaluate the classification accuracy of the proposed method. The experimental results show that the proposed method achieves more than 99 percent classification accuracy while remaining much simpler and faster than the DALI method.

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This paper presents a novel methodology for content-based search and retrieval of 3D objects. After proper positioning of the 3D objects using translation and scaling, a set of functionals is applied to the 3D model producing a new domain of concentric spheres. In this new domain, a new set of functionals is applied, resulting in a descriptor vector which is completely rotation invariant and thus suitable for 3D model matching. Further, weights are assigned to each descriptor, so as to significantly improve the retrieval results. Experiments on two different databases of 3D objects are performed so as to evaluate the proposed method in comparison with those most commonly cited in the literature. The experimental results show that the proposed method is superior in terms of precision versus recall and can be used for 3D model search and retrieval in a highly efficient manner.

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This paper presents a novel approach for fast rigid docking of proteins based on geometric complementarity. After extraction of the 3D molecular surface, a set of local surface patches is generated based on the local surface curvature. The shape complementarity between a pair of patches is calculated using an efficient shape descriptor, the Shape Impact Descriptor. The key property of the Shape Impact Descriptor is its rotation invariance, which obviates the need for taking an exhaustive set of rotations for each pair of patches. Thus, complementarity matching between two patches is reduced to a simple histogram matching. Finally, a condensed set of almost complementary pairs of surface patches is supplied as input to the final scoring step, where each pose is evaluated using a 3D distance grid. The experimental results prove that the proposed method demonstrates superior performance over other well-known geometry-based, rigid-docking approaches.