Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
In this study, we describe the development of new machine learning models to predict inhibition of the enzyme 3-dehydroquinate dehydratase (DHQD). This enzyme is the third step of the shikimate pathway and is responsible for the synthesis of chorisma...
The identification of subtype-selective GPCR (G-protein coupled receptor) ligands is a challenging task. In this study, we developed a computational protocol to find compounds with 5-HTR versus 5-HTR selectivity. Our approach employs the hierarchical...
IEEE/ACM transactions on computational biology and bioinformatics
Mar 26, 2018
Although Deep learning algorithms have outperformed conventional methods in predicting the sequence specificities of DNA-protein binding, they lack to consider the dependencies among nucleotides and the diverse binding lengths for different transcrip...
Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neura...
Journal of chemical information and modeling
Feb 8, 2018
Protein-ATP interactions are ubiquitous in a wide variety of biological processes. Correctly locating ATP binding sites from protein information is an important but challenging task for protein function annotation and drug discovery. However, there i...
BACKGROUND: The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been ...
Cyclin-dependent kinase (CDK) is an interesting biological macromolecule due to its role in cell cycle progression, transcription control, and neuronal development, to mention the most studied biological activities. Furthermore, the availability of h...
Computational and mathematical methods in medicine
Jan 30, 2018
We propose a novel method that predicts binding of G-protein coupled receptors (GPCRs) and ligands. The proposed method uses hub and cycle structures of ligands and amino acid motif sequences of GPCRs, rather than the 3D structure of a receptor or si...
Journal of pharmaceutical and biomedical analysis
Dec 24, 2017
Protein glycation in the body is one of the main reasons of diabetes complications. The electrochemical studies on the inhibitory mechanism of glycation are rather scarce. Thus, it is important to investigate the role of electrochemistry in the glyca...