DbStRiPs: Database of structural repeats in proteins

Daisy: An integrated repeat protein curation service

Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for protein structure prediction and repeat classification that are useful for this process. However, no service contemplates required databases and software to supplement researching on repeat proteins. In this publication we present Daisy, an integrated repeat protein curation web service. This service can process Protein Data Bank (PDB) and the AlphaFold Database entries for tandem repeats identification. In addition, it uses an algorithm to search a sequence against a library of Pfam hidden Markov model (HMM). Repeat classifications are associated with the identified families through RepeatsDB. This prediction is considered for enhancing the ReUPred algorithm execution and hastening the repeat units identification process. The service can also operate every associated PDB and AlphaFold structure with a UniProt proteome registry. Availability: The Daisy web service is freely accessible at daisy.bioinformatica.org.

Diversity and features of proteins with structural repeats

The review provides information on proteins with structural repeats, including their classification, characteristics, functions, and relevance in disease development. It explores methods for identifying structural repeats and specialized databases. The review also highlights the potential use of repeat proteins as drug design scaffolds and discusses their evolutionary mechanisms.

Sequence and Structure-Based Analyses of Human Ankyrin Repeats

Ankyrin is one of the most abundant protein repeat families found across all forms of life. It is found in a variety of multi-domain and single domain proteins in humans with diverse number of repeating units. They are observed to occur in several functionally diverse proteins, such as transcriptional initiators, cell cycle regulators, cytoskeletal organizers, ion transporters, signal transducers, developmental regulators, and toxins, and, consequently, defects in ankyrin repeat proteins have been associated with a number of human diseases. In this study, we have classified the human ankyrin proteins into clusters based on the sequence similarity in their ankyrin repeat domains. We analyzed the amino acid compositional bias and consensus ankyrin motif sequence of the clusters to understand the diversity of the human ankyrin proteins. We carried out network-based structural analysis of human ankyrin proteins across different clusters and showed the association of conserved residues with topologically important residues identified by network centrality measures. The analysis of conserved and structurally important residues helps in understanding their role in structural stability and function of these proteins. In this paper, we also discuss the significance of these conserved residues in disease association across the human ankyrin protein clusters.

TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner

The Tandem Repeat Annotation Library (TRAL) focuses on analyzing tandem repeat units in genomic sequences. TRAL can integrate and harmonize tandem repeat annotations from a large number of external tools, and provides a statistical model for evaluating and filtering the detected repeats. TRAL version 2.0 includes new features such as a module for identifying repeats from circular profile hidden Markov models, a new repeat alignment method based on the progressive Poisson Indel Process, an improved installation procedure and a docker container. TRAL is an open-source Python 3 library and is available, together with documentation and tutorials viavital-it.ch/software/tral.