MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery.

MOTIVATION: Identification of interactions between bioactive small molecules and target proteins is crucial for novel drug discovery, drug repurposing and uncovering off-target effects. Due to the tremendous size of the chemical space, experimental bioactivity screening efforts require the aid of computational approaches. Although deep learning models have been successful in predicting bioactive compounds, effective and comprehensive featurization of proteins, to be given as input to deep neural networks, remains a challenge. RESULTS: Here, we present a novel protein featurization approach to be used in deep learning-based compound-target protein binding affinity prediction. In the proposed method, multiple types of protein features such as sequence, structural, evolutionary and physicochemical properties are incorporated within multiple 2D vectors, which is then fed to state-of-the-art pairwise input hybrid deep neural networks to predict the real-valued compound-target protein interactions. The method adopts the proteochemometric approach, where both the compound and target protein features are used at the input level to model their interaction. The whole system is called MDeePred and it is a new method to be used for the purposes of computational drug discovery and repositioning. We evaluated MDeePred on well-known benchmark datasets and compared its performance with the state-of-the-art methods. We also performed in vitro comparative analysis of MDeePred predictions with selected kinase inhibitors' action on cancer cells. MDeePred is a scalable method with sufficiently high predictive performance. The featurization approach proposed here can also be utilized for other protein-related predictive tasks. AVAILABILITY AND IMPLEMENTATION: The source code, datasets, additional information and user instructions of MDeePred are available at https://github.com/cansyl/MDeePred. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Silhouette-based 3-D model reconstruction from multiple images.

The goal of this study is to investigate the reconstruction of three-dimensional (3-D) graphical models of real objects in a controlled imaging environment and present the work done in our group based on silhouette-based reconstruction. Although many parts of the whole system have been well-known in the literature and in practice, the main contribution of the paper is that it describes a complete, end-to-end system explained in detail. Based on a multi-image calibration method, an algorithm to extract the rotation axis of a turn-table has been developed. Furthermore, this can be extended to estimate robustly the initial bounding volume of the object to be modeled. The disadvantages of the silhouette-based reconstruction can be removed by an algorithm using photoconsistency. This algorithm has a simpler visibility check, and it eliminates the selection of threshold existing in similar algorithms. Besides, in order to construct the appearance, we use the concept of particles. The reconstruction results are shown both on real world and synthetic objects.

Subband domain coding of binary textual images for document archiving.

In this work, a subband domain textual image compression method is developed. The document image is first decomposed into subimages using binary subband decompositions. Next, the character locations in the subbands and the symbol library consisting of the character images are encoded. The method is suitable for keyword search in the compressed data. It is observed that very high compression ratios are obtained with this method. Simulation studies are presented.