Protein nitrotyrosine is an essential post-translational modification that results from the nitration of tyrosine amino acid residues. This modification is known to be associated with the regulation and characterization of several biological function...
Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for their application in industrial settings, an endeavour that is challenging and laborious. To address th...
The field of computational protein engineering has been transformed by recent advancements in machine learning, artificial intelligence, and molecular modeling, enabling the design of proteins with unprecedented precision and functionality. Computati...
We present a novel system that leverages curators in the loop to develop a dataset and model for detecting structure features and functional annotations at residue-level from standard publication text. Our approach involves the integration of data fr...
Accurate prediction of drug-target binding affinity (DTA) is essential in the field of drug discovery. Recently, scientists have been attempting to utilize artificial intelligence prediction to screen out a significant number of ineffective compounds...
Journal of chemical information and modeling
Sep 16, 2024
Identifying druggable binding sites on proteins is an important and challenging problem, particularly for cryptic, allosteric binding sites that may not be obvious from X-ray, cryo-EM, or predicted structures. The Site-Identification by Ligand Compet...
Protein secondary structure prediction (PSSP) plays a crucial role in resolving protein functions and properties. Significant progress has been made in this field in recent years, and the use of a variety of protein-related features, including amino ...
Generative deep learning models enable data-driven de novo design of molecules with tailored features. Chemical language models (CLM) trained on string representations of molecules such as SMILES have been successfully employed to design new chemical...
International journal of molecular sciences
Sep 8, 2024
Protein dynamics play a crucial role in biological function, encompassing motions ranging from atomic vibrations to large-scale conformational changes. Recent advancements in experimental techniques, computational methods, and artificial intelligence...
We here introduce Ensemble Optimizer (EnOpt), a machine-learning tool to improve the accuracy and interpretability of ensemble virtual screening (VS). Ensemble VS is an established method for predicting protein/small-molecule (ligand) binding. Unlike...