The eukaryotic proteome is shaped by E3 ubiquitin ligases targeting C-terminal degrons

I Koren, RT Timms, T Kula, Q Xu, MZ Li, SJ Elledge - Cell, 2018 - cell.com
Degrons are minimal elements that mediate the interaction of proteins with degradation
machineries to promote proteolysis. Despite their central role in proteostasis, the number of …

NAPS: network analysis of protein structures

B Chakrabarty, N Parekh - Nucleic acids research, 2016 - academic.oup.com
Traditionally, protein structures have been analysed by the secondary structure architecture
and fold arrangement. An alternative approach that has shown promise is modelling …

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes

F Cadet, N Fontaine, G Li, J Sanchis… - Scientific reports, 2018 - nature.com
Directed evolution is an important research activity in synthetic biology and biotechnology.
Numerous reports describe the application of tedious mutation/screening cycles for the …

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

L Paladin, M Bevilacqua, S Errigo… - Nucleic Acids …, 2021 - academic.oup.com
The RepeatsDB database (URL: https://repeatsdb. org/) provides annotations and
classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein …

Tandem repeats in proteins: prediction algorithms and biological role

M Pellegrini - Frontiers in bioengineering and biotechnology, 2015 - frontiersin.org
Tandem repetitions in protein sequence and structure is a fascinating subject of research
which has been a focus of study since the late 1990s. In this survey, we give an overview on …

Unusual structural and functional features of TpLRR/BspA-like LRR proteins

A Takkouche, X Qiu, M Sedova, L Jaroszewski… - Journal of Structural …, 2023 - Elsevier
Abstract Leucine Rich Repeat (LRR) domains, are present in hundreds of thousands of
proteins across all kingdoms of life and are typically involved in protein–protein interactions …

Structural and energetic characterization of the ankyrin repeat protein family

RG Parra, R Espada, N Verstraete… - PLoS computational …, 2015 - journals.plos.org
Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually
implicated in specific protein-protein interactions, these proteins are readily amenable for …

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

L Paladin, L Hirsh, D Piovesan… - Nucleic acids …, 2017 - academic.oup.com
Abstract RepeatsDB 2.0 (URL: http://repeatsdb. bio. unipd. it/) is an update of the database
of annotated tandem repeat protein structures. Repeat proteins are a widespread class of …

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

SE Bliven, A Lafita, PW Rose, G Capitani… - PLoS computational …, 2019 - journals.plos.org
Many proteins fold into highly regular and repetitive three dimensional structures. The
analysis of structural patterns and repeated elements is fundamental to understand protein …

Identifying tandem Ankyrin repeats in protein structures

B Chakrabarty, N Parekh - BMC bioinformatics, 2014 - Springer
Background Tandem repetition of structural motifs in proteins is frequently observed across
all forms of life. Topology of repeating unit and its frequency of occurrence are associated to …