Pubcasts in Structural Bioinformatics

Rethinking proteasome evolution: two novel bacterial proteasomes.
The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary....

Antibody-protein interactions: benchmark datasets and prediction tools evaluation
Background The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and...

Multipolar representation of protein structure
Background That the structure determines the function of proteins is a central paradigm in biology. However, protein functions are more directly related to cooperative...

Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry
Because of the rise in atmospheric oxygen 2.3 billion years ago (Gya) and the subsequent changes in oceanic redox state over the last 2.3–1 Gya, trace metal bioavailability in marine...

The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis
Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists...

Wiggle—Predicting Functionally Flexible Regions from Primary Sequence
The Wiggle series are support vector machine–based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are...

Phylogeny determined by protein domain content
A simple classification scheme that uses only the presence or absence of a protein domain architecture has been used to determine the phylogeny of 174 complete genomes. The method correctly divides...

Structural Evolution of the Protein Kinase–Like Superfamily
The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all...