Structure-based pharmacophore models are often developed by selecting a single protein-ligand complex with good resolution and better binding affinity data which prevents the analysis of other structures having a similar potential to act as better te...
Medical & biological engineering & computing
Mar 18, 2022
Computer-aided rational vaccine design (RVD) and synthetic pharmacology are rapidly developing fields that leverage existing datasets for developing compounds of interest. Computational proteomics utilizes algorithms and models to probe proteins for ...
Journal of chemical theory and computation
Mar 15, 2022
Protonation states of ionizable protein residues modulate many essential biological processes. For correct modeling and understanding of these processes, it is crucial to accurately determine their p values. Here, we present four tree-based machine l...
BACKGROUND: Current protein family modeling methods like profile Hidden Markov Model (pHMM), k-mer based methods, and deep learning-based methods do not provide very accurate protein function prediction for proteins in the twilight zone, due to low s...
Human DNA sequencing has revealed numerous single nucleotide variants associated with complex diseases. Researchers have shown that these variants have potential effects on protein function, one of which is to disrupt protein phosphorylation. Based o...
Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be ...
Measuring evolutionary rates at the residue level is indispensable for gaining structural and functional insights into proteins. State-of-the-art tools for estimating rates take as input a large set of homologous proteins, a probabilistic model of ev...
Accurate prediction of binding poses is crucial to structure-based drug design. We employ two powerful artificial intelligence (AI) approaches, data-mining and machine-learning, to design artificial neural network (ANN) based pose-scoring function. I...
International journal of molecular sciences
Mar 9, 2022
BACKGROUND: For decades, the rate of solving new biomolecular structures has been exceeding that at which their manual classification and feature characterisation can be carried out efficiently. Therefore, a new comprehensive and holistic tool for th...
Proceedings of the National Academy of Sciences of the United States of America
Mar 7, 2022
SignificanceComputational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level geom...
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