International journal of molecular sciences
Oct 16, 2022
Peptide detectability is defined as the probability of identifying a peptide from a mixture of standard samples, which is a key step in protein identification and analysis. Exploring effective methods for predicting peptide detectability is helpful f...
A fundamental question in protein science is where allosteric hotspots - residues critical for allosteric signaling - are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allo...
Imaging is commonly used as a characterization method in the pharmaceuticals industry, including for quantifying subvisible particles in solid and liquid formulations. Extracting information beyond particle size, such as classifying morphological sub...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 10, 2022
Identification of drug-target interaction (DTI) is the most important issue in the broad field of drug discovery. Using purely biological experiments to verify drug-target binding profiles takes lots of time and effort, so computational technologies ...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 10, 2022
Protein fold recognition contribute to comprehend the function of proteins, which is of great help to the gene therapy of diseases and the development of new drugs. Researchers have been working in this direction and have made considerable achievemen...
IEEE journal of biomedical and health informatics
Oct 4, 2022
After the development of next-generation sequencing techniques, protein sequences are abundantly available. Determining the functional characteristics of these proteins is costly and time-consuming. The gap between the number of protein sequences and...
AlphaFold2 and related computational systems predict protein structure using deep learning and co-evolutionary relationships encoded in multiple sequence alignments (MSAs). Despite high prediction accuracy achieved by these systems, challenges remain...
Computational and mathematical methods in medicine
Oct 3, 2022
Water molecules play an important role in many biological processes in terms of stabilizing protein structures, assisting protein folding, and improving binding affinity. It is well known that, due to the impacts of various environmental factors, it ...
Mathematical biosciences and engineering : MBE
Sep 30, 2022
The development of new drugs is a long and costly process, Computer-aided drug design reduces development costs while computationally shortening the new drug development cycle, in which DTA (Drug-Target binding Affinity) prediction is a key step to s...
Journal of chemical information and modeling
Sep 29, 2022
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component analysis for red...
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