The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact prediction even f...
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...
For rational drug design, it is essential to predict the binding mode of protein-ligand complexes. Although various machine learning-based models have been reported that use convolutional neural networks (deep learning) to predict binding modes from ...
The journal of physical chemistry letters
Aug 14, 2019
Longevity is a very important and interesting topic, and has been demonstrated to be related to longevity. We combined network pharmacology, machine learning, deep learning, and molecular dynamics (MD) simulation to investigate potent lead drugs. Re...
The decoding of transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF labels into the same space. By training on binding data f...
The journal of physical chemistry letters
Jul 22, 2019
It has been demonstrated that MMP13 enzyme is related to most cancer cell tumors. The world's largest traditional Chinese medicine database was applied to screen for structure-based drug design and ligand-based drug design. To predict drug activity, ...
Journal of molecular graphics & modelling
Jul 15, 2019
Membrane proteins, the most important drug targets, account for around 30% of total proteins encoded by the genome of living organisms. An important role of these proteins is to bind adenosine triphosphate (ATP), facilitating crucial biological proce...
International journal of molecular sciences
Jul 12, 2019
Transcription factor binding sites (TFBSs) play an important role in gene expression regulation. Many computational methods for TFBS prediction need sufficient labeled data. However, many transcription factors (TFs) lack labeled data in cell types. W...
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...