It has been a landmark year for artificial intelligence (AI) and biotechnology. Perhaps the most noteworthy of these advances was Google DeepMind's AlphaFold2 algorithm which smashed records in protein structure prediction (Jumper et al., 2021, Natur...
Deep learning using neural networks relies on a class of machine-learnable models constructed using 'differentiable programs'. These programs can combine mathematical equations specific to a particular domain of natural science with general-purpose, ...
Graph representations are traditionally used to represent protein structures in sequence design protocols in which the protein backbone conformation is known. This infrequently extends to machine learning projects: existing graph convolution algorith...
Protein amino acid sequences can be used to determine the functions of the protein. However, determining the function of a single protein requires many resources and a tremendous amount of time. Computational Intelligence methods such as Deep learnin...
In this paper, we report our tFold framework's performance on the inter-residue contact prediction task in the 14th Critical Assessment of protein Structure Prediction (CASP14). Our tFold framework seamlessly combines both homologous sequences and st...
Many researchers have recently used the prediction of protein secondary structure (local conformational states of amino acid residues) to test advances in predictive and machine learning technology such as Neural Net Deep Learning. Protein secondary ...
Journal of chemical theory and computation
Sep 23, 2021
Scoring functions are the essential component in molecular docking methods. An accurate scoring function is expected to distinguish the native ligand pose from decoy poses. Our previous experience (Pei et al. 2019, 59 (7), 3305-3315) proved that com...
Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protei...
Since the first revelation of proteins functioning as macromolecular machines through their three dimensional structures, researchers have been intrigued by the marvelous ways the biochemical processes are carried out by proteins. The aspiration to u...
Medical & biological engineering & computing
Sep 20, 2021
Advances in high-throughput techniques lead to evolving a large number of unknown protein sequences (UPS). Functional characterization of UPS is significant for the investigation of disease symptoms and drug repositioning. Protein subcellular localiz...