Selecting a non‐redundant representative subset of sequences is a common step in many
bioinformatics workflows, such as the creation of non‐redundant training sets for sequence …

Motivation: The size of current protein databases is a challenge for many Bioinformatics
applications, both in terms of processing speed and information redundancy. It may be …

Hierarchical classification is probably the most popular approach to group-related proteins.
However, there are a number of problems associated with its use for this purpose. One is …

Diversification libraries of protein sequences that contain a similar set of structures over a
variety of sequences can help protein design pipelines by introducing flexibility into the …

Abstract Motivation Multiple sequence alignments (MSAs) can provide essential input to
many bioinformatics applications, including protein structure prediction and functional …

Protein sequence similarity searching programs like BLASTP, SSEARCH, and FASTA use
scoring matrices that are designed to identify distant evolutionary relationships (BLOSUM62 …

Every program for searching protein sequences against a database includes a choice of a
protein weight matrix, also called a scoring matrix. Weight matrices add sensitivity to the …

Motivation Discrete features can be obtained from protein sequences using a feature
extraction method. These features are the basis of downstream processing of protein data …

Motivation: Evolutionarily conserved amino acids within proteins characterize functional or
structural regions. Conversely, less conserved amino acids within these regions are …

Finding backbone substructures from the Protein Data Bank that match an arbitrary query
structural motif, composed of multiple disjoint segments, is a problem of growing relevance …