Over the past few decades, the number of available structural bioinformatics pipelines,
libraries, plugins, web resources and software has increased exponentially and become …

Applied biocatalysis is driven by environmental and economic incentives for using enzymes
in the synthesis of various pharmaceutical and industrially important chemicals. Protein …

Motivation In addition to substitution frequency data from protein sequence alignments,
many state-of-the-art methods for contact prediction rely on additional sources of …

Motivation Significant improvements in the prediction of protein residue–residue contacts
are observed in the recent years. These contacts, predicted using a variety of coevolution …

The accuracy of sequence‐based tertiary contact predictions was assessed in a blind
prediction experiment at the CASP13 meeting. After 4 years of significant improvements in …

Motivation Residue contact prediction was revolutionized recently by the introduction of
direct coupling analysis (DCA). Further improvements, in particular for small families, have …

Computational elucidation of membrane protein (MP) structures is challenging partially due
to lack of sufficient solved structures for homology modeling. Here, we describe a high …

Motivation Exciting new opportunities have arisen to solve the protein contact prediction
problem from the progress in neural networks and the availability of a large number of …

We apply the tensor train (TT) decomposition to construct the tensor product polynomial
chaos expansion (PCE) of a random field, to solve the stochastic elliptic diffusion PDE with …

Potts statistical models have become a popular and promising way to analyze mutational
covariation in protein multiple sequence alignments (MSAs) in order to understand protein …