Current opinion in structural biology
Feb 26, 2021
Machine learning (ML) can expedite directed evolution by allowing researchers to move expensive experimental screens in silico. Gathering sequence-function data for training ML models, however, can still be costly. In contrast, raw protein sequence d...
Cysteine (Cys) is the most reactive amino acid participating in a wide range of biological functions. In-silico predictions complement the experiments to meet the need of functional characterization. Multiple Cys function prediction algorithm is scar...
The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million dat...
Understanding the function of protein is conducive to research in advanced fields such as gene therapy of diseases, the development and design of new drugs, etc. The prerequisite for understanding the function of a protein is to determine its tertiar...
The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achie...
Identification of thermostable and alkaline xylanases from different fungal and bacterial species have gained an interest for the researchers because of its biotechnological relevance in many industries, such as pulp, paper, and bioethanol. In this s...
The protein disulfide bond is a covalent bond that forms during post-translational modification by the oxidation of a pair of cysteines. In protein, the disulfide bond is the most frequent covalent link between amino acids after the peptide bond. It ...
International journal of molecular sciences
Jan 19, 2021
Accurately identifying protein-ATP binding residues is important for protein function annotation and drug design. Previous studies have used classic machine-learning algorithms like support vector machine (SVM) and random forest to predict protein-AT...
The identification of SARS-CoV-2-specific T cell receptor (TCR) sequences is critical for understanding T cell responses to SARS-CoV-2. Accordingly, we reanalyze publicly available data from SARS-CoV-2-recovered patients who had low-severity disease ...
Many therapeutic drugs are compounds that can be represented by simple chemical structures, which contain important determinants of affinity at the site of action. Recently, graph convolutional neural network (GCN) models have exhibited excellent res...