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...
As an important task in protein structure and function studies, protein fold recognition has attracted more and more attention. The existing computational predictors in this field treat this task as a multi-classification problem, ignoring the relati...
Protein fold recognition is one of the most critical tasks to explore the structures and functions of the proteins based on their primary sequence information. The existing protein fold recognition approaches rely on features reflecting the character...
Protein fold recognition is critical for studying the structures and functions of proteins. The existing protein fold recognition approaches failed to efficiently calculate the pairwise sequence similarity scores of the proteins in the same fold shar...
We describe AlphaFold, the protein structure prediction system that was entered by the group A7D in CASP13. Submissions were made by three free-modeling (FM) methods which combine the predictions of three neural networks. All three systems were guide...
MOTIVATION: The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, define...
MOTIVATION: Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a te...
MOTIVATION: Recent CASP experiments have witnessed exciting progress on folding large-size non-humongous proteins with the assistance of co-evolution based contact predictions. The success is however anecdotal due to the requirement of the contact pr...
MOTIVATION: Protein fold classification is a critical step in protein structure prediction. There are two possible ways to classify protein folds. One is through template-based fold assignment and the other is ab-initio prediction using machine learn...