MOTIVATION: Identifying the binding sites of antibodies is essential for developing vaccines and synthetic antibodies. In this article, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the ...
Protein science : a publication of the Protein Society
Jul 1, 2024
Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (A...
Methods from artificial intelligence (AI) trained on large datasets of sequences and structures can now "write" proteins with new shapes and molecular functions de novo, without starting from proteins found in nature. In this Perspective, I will disc...
Protein engineering, design & selection : PEDS
Jan 29, 2024
Deep learning methods for protein sequence design focus on modeling and sampling the many- dimensional distribution of amino acid sequences conditioned on the backbone structure. To produce physically foldable sequences, inter-residue couplings need ...
Understanding the interactions between a ligand and its molecular target is crucial in guiding the optimization of molecules for any drug design workflow. Multiple experimental and computational methods have been developed to better understand these...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2024
Protein-protein interactions are involved in almost all processes in a living cell and determine the biological functions of proteins. To obtain mechanistic understandings of protein-protein interactions, the tertiary structures of protein complexes ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2024
An exponential increase in the number of publications that address artificial intelligence (AI) usage in life sciences has been noticed in recent years, while new modeling techniques are constantly being reported. The potential of these methods is va...
The protein folding mechanisms are crucial to understanding the fundamental processes of life and solving many biological and medical problems. By studying the folding process, we can reveal how proteins achieve their biological functions through spe...
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