Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent...
As with other proteins, the conformation of the silk protein is critical for determining the mechanical, optical and biological performance of materials. However, an efficient, accurate and time-efficient method for evaluating the protein conformatio...
Proceedings of the National Academy of Sciences of the United States of America
Apr 13, 2021
In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth ...
Proceedings of the National Academy of Sciences of the United States of America
Mar 16, 2021
The protein design problem is to identify an amino acid sequence that folds to a desired structure. Given Anfinsen's thermodynamic hypothesis of folding, this can be recast as finding an amino acid sequence for which the desired structure is the lowe...
Artificial intelligence (AI)-based approaches have had indubitable impact across the sciences through the ability to extract relevant information from raw data. Recently, AI has also found use in enhancing the efficiency of molecular simulations, whe...
MusiteDeep is an online resource providing a deep-learning framework for protein post-translational modification (PTM) site prediction and visualization. The predictor only uses protein sequences as input and no complex features are needed, which res...
MOTIVATION: Antibody structure is largely conserved, except for a complementarity-determining region featuring six variable loops. Five of these loops adopt canonical folds which can typically be predicted with existing methods, while the remaining l...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2020
Identifying residue-residue contacts in protein-protein interactions or complex is crucial for understanding protein and cell functions. DCA (direct-coupling analysis) methods shed some light on this, but they need many sequence homologs to yield acc...