Improved Protein Real-Valued Distance Prediction Using Deep Residual Dense Network (DRDN)

Abstract

Three-dimensional protein structure prediction is one of the major challenges in bioinformatics. According to recent research findings, real-valued distance prediction plays a vital role in determining the unique three-dimensional protein structure. This paper proposes a novel methodology involving a deep residual dense network (DRDN) for predicting protein real-valued distance. The features extracted from the given query protein sequence and its corresponding homologous sequences are used for training the model. Multi-aligned homologous sequences for each query protein sequence are retrieved from five different databases using DeepMSA, HHblits, and HITS_PR_HHblits methods. The proposed method yielded outcomes of 3.89, 0.23, 0.45, and 0.63, respectively, corresponding to the evaluation metrics such as Absolute Error, Relative Error, High-accuracy Pairwise Distance Test (PDA), and Pairwise Distance Test (PDT). Further, the contact map is computed based on CASP criteria by converting the predicted real-valued distance, and it is evaluated using the precision metric. It is observed that precision of long-range top L/5 contact prediction on the CASP13 dataset by the proposed method, RaptorX, Zhang, trRosetta, JinboXu & JinLu, and Deepdist are 0.834, 0.657, 0.70, 0.785, 0.786, and 0.812, respectively. Also, Top-L/5 contact prediction on the CASP14 dataset evaluated using average precision resulted in 0.847, 0.707, 0.752, 0.783, 0.792, 0.817, and 0.825 respectively, corresponding to the proposed method, Zhang, RaptorX, trRosetta, Deepdist, JinboXu & JinLu, and Alphafold2.