In this paper, using Word2vec, a widely-used natural language processing method, we demonstrate that protein domains may have a learnable implicit semantic "meaning" in the context of their functional contributions to the multi-domain proteins in whi...
Protein structure prediction has long been available as an alternative to experimental structure determination, especially via homology modeling based on templates from related sequences. Recently, models based on distance restraints from coevolution...
Proteins play important roles in living organisms, and their function is directly linked with their structure. Due to the growing gap between the number of proteins being discovered and their functional characterization (in particular as a result of ...
Protein engineering and synthetic biology stand to benefit immensely from recent advances in silico tools for structural and functional analyses of proteins. In the context of designing novel proteins, current in silico tools inform the user on indiv...
Although many structural bioinformatics tools have been using neural network models for a long time, deep neural network (DNN) models have attracted considerable interest in recent years. Methods employing DNNs have had a significant impact in recent...
This paper reports the CASP13 results of distance-based contact prediction, threading, and folding methods implemented in three RaptorX servers, which are built upon the powerful deep convolutional residual neural network (ResNet) method initiated by...
Protein phosphorylation is one of the essential posttranslation modifications playing a vital role in the regulation of many fundamental cellular processes. We propose a LightGBM-based computational approach that uses evolutionary, geometric, sequenc...
Sequence based DNA-binding protein (DBP) prediction is a widely studied biological problem. Sliding windows on position specific substitution matrices (PSSMs) rows predict DNA-binding residues well on known DBPs but the same models cannot be applied ...
Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites throu...
The ability to predict local structural features of a protein from the primary sequence is of paramount importance for unraveling its function in absence of experimental structural information. Two main factors affect the utility of potential predict...