Journal of computer-aided molecular design
Mar 22, 2022
Modern molecular docking comprises the prediction of pose and affinity. Prediction of docking poses is required for affinity prediction when three-dimensional coordinates of the ligand have not been provided. However, a large number of feature engine...
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...
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...
Prediction of side chain conformations of amino acids in proteins (also termed "packing") is an important and challenging part of protein structure prediction with many interesting applications in protein design. A variety of methods for packing have...
We examined the ability of two human cytosolic transaminases, aspartate aminotransferase (GOT1) and alanine aminotransferase (GPT), to transform their preferred substrates whilst discriminating against similar metabolites. This offers an opportunity ...
A protein backbone structure is designable if a substantial number of amino acid sequences exist that autonomously fold into it. It has been suggested that the designability of backbones is governed mainly by side chain-independent or side chain type...
Bolstered by recent methodological and hardware advances, deep learning has increasingly been applied to biological problems and structural proteomics. Such approaches have achieved remarkable improvements over traditional machine learning methods in...
DeepMind released AlphaFold 2.0 in 2020, an artificial intelligence model to predict the structure of proteins, which could mean that proteins can be characterized without the need for tedious and costly lab analysis.
Journal of computational biology : a journal of computational molecular cell biology
Jan 21, 2022
Template-based modeling (TBM), including homology modeling and protein threading, is one of the most reliable techniques for protein structure prediction. It predicts protein structure by building an alignment between the query sequence under predict...