We investigate the effect of aligner choice on inferences of positive selection using site-
specific models of molecular evolution. We find that independently of the choice of aligner …

The development and validation of computational macromolecular modeling and design
methods depend on suitable benchmark datasets and informative metrics for comparing …

The notion of using the evolutionary history encoded within multiple sequence alignments to
predict allosteric mechanisms is appealing. In this approach, correlated mutations are …

Motivation: Multiple sequence alignment (MSA) is a core method in bioinformatics. The
accuracy of such alignments may influence the success of downstream analyses such as …

Sampling alternative conformations is key to understanding how proteins work and
engineering them for new functions. However, accurately characterizing and modeling …

Amino acid covariation, where the identities of amino acids at different sequence positions
are correlated, is a hallmark of naturally occurring proteins. This covariation can arise from …

The active sites of enzymes consist of residues necessary for catalysis and structurally
important noncatalytic residues that together maintain the architecture and function of the …

Ancestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a
phylogeny describing the history of the protein family and a model of the molecular …

Background A standard procedure in many areas of bioinformatics is to use a single multiple
sequence alignment (MSA) as the basis for various types of analysis. However, downstream …

Adenylyl cyclase (AC) toxin is an essential toxin that allows Bordetella pertussis to invade
eukaryotic cells, where it is activated after binding to calmodulin (CaM). Based on the crystal …