Adaptable hydrogel networks with reversible linkages for tissue engineering

H Wang, SC Heilshorn - Advanced Materials, 2015 - Wiley Online Library
Adaptable hydrogels have recently emerged as a promising platform for three‐dimensional
(3D) cell encapsulation and culture. In conventional, covalently crosslinked hydrogels …

Protein engineering by combined computational and in vitro evolution approaches

L Rosenfeld, M Heyne, JM Shifman, N Papo - Trends in biochemical …, 2016 - cell.com
Two alternative strategies are commonly used to study protein–protein interactions (PPIs)
and to engineer protein-based inhibitors. In one approach, binders are selected …

The multiple‐specificity landscape of modular peptide recognition domains

D Gfeller, F Butty, M Wierzbicka… - Molecular systems …, 2011 - embopress.org
Modular protein interaction domains form the building blocks of eukaryotic signaling
pathways. Many of them, known as peptide recognition domains, mediate protein …

Data-driven prediction and design of bZIP coiled-coil interactions

V Potapov, JB Kaplan, AE Keating - PLoS computational biology, 2015 - journals.plos.org
Selective dimerization of the basic-region leucine-zipper (bZIP) transcription factors presents
a vivid example of how a high degree of interaction specificity can be achieved within a …

Predicting PDZ domain mediated protein interactions from structure

S Hui, X Xing, GD Bader - BMC bioinformatics, 2013 - Springer
Background PDZ domains are structural protein domains that recognize simple linear amino
acid motifs, often at protein C-termini, and mediate protein-protein interactions (PPIs) in …

Computational tools and strategies to develop peptide-based inhibitors of protein-protein interactions

M Delaunay, T Ha-Duong - Computational peptide science: methods and …, 2021 - Springer
Protein-protein interactions play crucial and subtle roles in many biological processes and
modifications of their fine mechanisms generally result in severe diseases. Peptide …

[HTML][HTML] Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains

J Teyra, SS Sidhu, PM Kim - FEBS letters, 2012 - Elsevier
Peptide-binding domains play a critical role in regulation of cellular processes by mediating
protein interactions involved in signalling. In recent years, the development of large-scale …

[HTML][HTML] Domain-mediated protein interaction prediction: From genome to network

J Reimand, S Hui, S Jain, B Law, GD Bader - FEBS letters, 2012 - Elsevier
Protein–protein interactions (PPIs), involved in many biological processes such as cellular
signaling, are ultimately encoded in the genome. Solving the problem of predicting protein …

Fast and reliable prediction of domain–peptide binding affinity using coarse-grained structure models

F Tian, R Tan, T Guo, P Zhou, L Yang - Biosystems, 2013 - Elsevier
Domain–peptide recognition and interaction are fundamentally important for eukaryotic
signaling and regulatory networks. It is thus essential to quantitatively infer the binding …

Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets

EF Tahti, JM Blount, SN Jackson, M Gao… - Protein …, 2023 - Wiley Online Library
Protein–protein interactions that involve recognition of short peptides are critical in cellular
processes. Protein–peptide interaction surface areas are relatively small and shallow, and …