[HTML][HTML] FoldX as protein engineering tool: better than random based approaches?

O Buß, J Rudat, K Ochsenreither - Computational and structural …, 2018 - Elsevier
Improving protein stability is an important goal for basic research as well as for clinical and
industrial applications but no commonly accepted and widely used strategy for efficient …

Peptide inhibitors targeting protein kinases

H Eldar-Finkelman, M Eisenstein - Current pharmaceutical …, 2009 - ingentaconnect.com
Phosphorylation by protein kinases is a central theme in biological systems. Aberrant protein
kinase activity has been implicated in a variety of human diseases, therefore, modulation of …

Phosphorylation in protein-protein binding: effect on stability and function

H Nishi, K Hashimoto, AR Panchenko - Structure, 2011 - cell.com
Posttranslational modifications offer a dynamic way to regulate protein activity, subcellular
localization, and stability. Here we estimate the effect of phosphorylation on protein binding …

Design of protein-interaction specificity gives selective bZIP-binding peptides

G Grigoryan, AW Reinke, AE Keating - Nature, 2009 - nature.com
Interaction specificity is a required feature of biological networks and a necessary
characteristic of protein or small-molecule reagents and therapeutics. The ability to alter or …

AB‐bind: antibody binding mutational database for computational affinity predictions

S Sirin, JR Apgar, EM Bennett, AE Keating - Protein Science, 2016 - Wiley Online Library
Antibodies (Abs) are a crucial component of the immune system and are often used as
diagnostic and therapeutic agents. The need for high‐affinity and high‐specificity antibodies …

[HTML][HTML] Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking

M Blaszczyk, M Kurcinski, M Kouza, L Wieteska… - Methods, 2016 - Elsevier
Protein–peptide interactions play essential functional roles in living organisms and their
structural characterization is a hot subject of current experimental and theoretical research …

Accurate prediction of peptide binding sites on protein surfaces

E Petsalaki, A Stark, E García-Urdiales… - PLoS computational …, 2009 - journals.plos.org
Many important protein–protein interactions are mediated by the binding of a short peptide
stretch in one protein to a large globular segment in another. Recent efforts have provided …

Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin

TR Caulfield, FC Fiesel… - PLoS computational …, 2014 - journals.plos.org
Loss-of-function mutations in PINK1 or PARKIN are the most common causes of autosomal
recessive Parkinson's disease. Both gene products, the Ser/Thr kinase PINK1 and the E3 …

MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles

M Tiberti, T Terkelsen, K Degn, L Beltrame… - Briefings in …, 2022 - academic.oup.com
Mutations, which result in amino acid substitutions, influence the stability of proteins and
their binding to biomolecules. A molecular understanding of the effects of protein mutations …

Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases

A Zeke, T Bastys, A Alexa, Á Garai… - Molecular systems …, 2015 - embopress.org
Mitogen‐activated protein kinases (MAPK) are broadly used regulators of cellular signaling.
However, how these enzymes can be involved in such a broad spectrum of physiological …