Motivation
Inter-protein (interfacial) contact prediction is very useful for in silico structural characterization of protein-protein interactions. Although deep learning has been applied to this problem, its accuracy is not as good as intra-protein contact prediction.
Results
We propose a new deep learning method GLINTER (Graph Learning of INTER-protein contacts) for interfacial contact prediction of dimers, leveraging a rotational invariant representation of protein tertiary structures and a pretrained language model of multiple sequence alignments (MSAs). Tested on the 13th and 14th CASP-CAPRI datasets, the average top L/10 precision achieved by GLINTER is 54% on the homodimers and 52% on all the dimers, much higher than 30% obtained by the latest deep learning method DeepHomo on the homodimers and 15% obtained by BIPSPI on all the dimers. Our experiments show that GLINTER-predicted contacts help improve selection of docking decoys.
Availability
The software is available at https://github.com/zw2x/glinter. The data sets are available at https://github.com/zw2x/glinter/data.
Recently, deep learning based single image superresolution(SR) approaches have achieved great development. The state-of-the-art SR methods usually adopt a feed-forward pipeline to establish a non-linear mapping between low-res(LR) and high-res(HR) images. However, due to treating all image regions equally without considering the difficulty diversity, these approaches meet an upper bound for optimization. To address this issue, we propose a novel SR approach that discriminately processes each image region within an image by its difficulty. Specifically, we propose a dual-way SR network that one way is trained to focus on easy image regions and another is trained to handle hard image regions. To identify whether a region is easy or hard, we propose a novel image difficulty recognition network based on PSNR prior. Our SR approach that uses the region mask to adaptively enforce the dual-way SR network yields superior results. Extensive experiments on several standard benchmarks (e.g., Set5, Set14, BSD100, and Urban100) show that our approach achieves state-of-the-art performance.
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