Structural and dynamic determinants of protein-peptide recognition

O Dagliyan, EA Proctor, KM D'Auria, F Ding… - Structure, 2011 - cell.com
Protein-peptide interactions play important roles in many cellular processes, including signal
transduction, trafficking, and immune recognition. Protein conformational changes upon …

The structural basis of peptide-protein binding strategies

N London, D Movshovitz-Attias, O Schueler-Furman - Structure, 2010 - cell.com
Peptide-protein interactions are very prevalent, mediating key processes such as signal
transduction and protein trafficking. How can peptides overcome the entropic cost involved …

Modelling peptide–protein complexes: docking, simulations and machine learning

A Mondal, L Chang, A Perez - QRB discovery, 2022 - cambridge.org
Peptides mediate up to 40% of protein interactions, their high specificity and ability to bind in
places where small molecules cannot make them potential drug candidates. However …

Exploring protein-peptide recognition pathways using a supervised molecular dynamics approach

V Salmaso, M Sturlese, A Cuzzolin, S Moro - Structure, 2017 - cell.com
Peptides have gained increased interest as therapeutic agents during recent years. The
high specificity and relatively low toxicity of peptide drugs derive from their extremely tight …

Improved modeling of peptide-protein binding through global docking and accelerated molecular dynamics simulations

J Wang, A Alekseenko, D Kozakov… - Frontiers in molecular …, 2019 - frontiersin.org
Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and
play a key role in cellular signaling, protein trafficking, immunology, and oncology. However …

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations

S Liang, L Li, WL Hsu, MN Pilcher, V Uversky… - Biochemistry, 2009 - ACS Publications
The significant work that has been invested toward understanding protein− protein
interaction has not translated into significant advances in structure-based predictions. In …

Recent advances in computational models for the study of protein–peptide interactions

D Kilburg, E Gallicchio - Advances in protein chemistry and structural …, 2016 - Elsevier
We review computational models and software tools in current use for the study of protein–
peptide interactions. Peptides and peptide derivatives are growing in interest as therapeutic …

Modeling peptide–protein interactions

N London, B Raveh, O Schueler-Furman - Homology Modeling: Methods …, 2012 - Springer
Peptide–protein interactions are prevalent in the living cell and form a key component of the
overall protein–protein interaction network. These interactions are drawing increasing …

Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how

N London, B Raveh, O Schueler-Furman - Current opinion in structural …, 2013 - Elsevier
Highlights•Accrual of peptide–protein complex structures allowed their detailed
characterization.•This has lead to rapid progress in peptide docking, based on diverse …

Coarse-grained simulations of protein-protein association: an energy landscape perspective

KM Ravikumar, W Huang, S Yang - Biophysical journal, 2012 - cell.com
Understanding protein-protein association is crucial in revealing the molecular basis of
many biological processes. Here, we describe a theoretical simulation pipeline to study …