Interfering peptides targeting protein–protein interactions: the next generation of drugs?

H Bruzzoni-Giovanelli, V Alezra, N Wolff, CZ Dong… - Drug Discovery …, 2018 - Elsevier
Highlights•Structure-based strategies allow more-specific targeting of protein–protein
interactions (PPIs).•Interfering peptides (IPs) become a promising alternative to small …

Harnessing protein folding neural networks for peptide–protein docking

T Tsaban, JK Varga, O Avraham, Z Ben-Aharon… - Nature …, 2022 - nature.com
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …

Computational design of peptide ligands

P Vanhee, AM van der Sloot, E Verschueren… - Trends in …, 2011 - cell.com
Peptides possess several attractive features when compared to small molecule and protein
therapeutics, such as high structural compatibility with target proteins, the ability to disrupt …

Sub‐angstrom modeling of complexes between flexible peptides and globular proteins

B Raveh, N London… - … : Structure, Function, and …, 2010 - Wiley Online Library
A wide range of regulatory processes in the cell are mediated by flexible peptides that fold
upon binding to globular proteins. Computational efforts to model these interactions are …

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

B Raveh, N London, L Zimmerman… - PloS one, 2011 - journals.plos.org
Flexible peptides that fold upon binding to another protein molecule mediate a large number
of regulatory interactions in the living cell and may provide highly specific recognition …

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

N Alam, O Goldstein, B Xia, KA Porter… - PLoS computational …, 2017 - journals.plos.org
Peptide-protein interactions contribute a significant fraction of the protein-protein
interactome. Accurate modeling of these interactions is challenging due to the vast …

Protein–protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction

H Rui, KS Ashton, J Min, C Wang, PR Potts - RSC Chemical Biology, 2023 - pubs.rsc.org
Molecular glues are a class of small molecules that stabilize the interactions between
proteins. Naturally occurring molecular glues are present in many areas of biology where …

The culprit behind amyloid beta peptide related neurotoxicity in Alzheimer's disease: oligomer size or conformation?

K Broersen, F Rousseau, J Schymkowitz - Alzheimer's research & therapy, 2010 - Springer
Since the reformulation of the amyloid cascade hypothesis to focus on oligomeric
aggregates of amyloid beta as the prime toxic species causing Alzheimer's disease, many …

Fully blind peptide-protein docking with pepATTRACT

CEM Schindler, SJ de Vries, M Zacharias - Structure, 2015 - cell.com
Peptide-protein interactions are ubiquitous in the cell and form an important part of the
interactome. Computational docking methods can complement experimental …

MDockPeP: An ab‐initio protein–peptide docking server

X Xu, C Yan, X Zou - Journal of computational chemistry, 2018 - Wiley Online Library
Protein–peptide interactions play a crucial role in a variety of cellular processes. The protein–
peptide complex structure is a key to understand the mechanisms underlying protein …