[HTML][HTML] Integrative modelling of biomolecular complexes

PI Koukos, A Bonvin - Journal of molecular biology, 2020 - Elsevier
In recent years, the use of integrative, information-driven computational approaches for
modeling the structure of biomolecules has been increasing in popularity. These are now …

Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease

GA Pantelopulos, CB Abraham… - Annual Review of …, 2024 - annualreviews.org
Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism
that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease …

Peptide permeation across a phosphocholine membrane: An atomically detailed mechanism determined through simulations and supported by experimentation

AE Cardenas, CI Drexler, R Nechushtai… - The Journal of …, 2022 - ACS Publications
Cell-penetrating peptides (CPPs) facilitate translocation across biological membranes and
are of significant biological and medical interest. Several CPPs can permeate into specific …

Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta

R Samanta, A Harmalkar, P Prathima… - Journal of Chemical …, 2024 - ACS Publications
The oligomerization of protein macromolecules on cell membranes plays a fundamental role
in regulating cellular function. From modulating signal transduction to directing immune …

Integrative modeling of membrane-associated protein assemblies

J Roel-Touris, B Jiménez-García… - Nature communications, 2020 - nature.com
Membrane proteins are among the most challenging systems to study with experimental
structural biology techniques. The increased number of deposited structures of membrane …

[HTML][HTML] Structure of APP-C991–99 and implications for role of extra-membrane domains in function and oligomerization

GA Pantelopulos, JE Straub, D Thirumalai… - Biochimica et Biophysica …, 2018 - Elsevier
The 99 amino acid C-terminal fragment of Amyloid Precursor Protein APP-C99 (C99) is
cleaved by γ-secretase to form Aβ peptide, which plays a critical role in the etiology of …

Protein–protein docking in drug design and discovery

AA Kaczor, D Bartuzi, TM Stępniewski… - … Drug Discovery and …, 2018 - Springer
Protein–protein interactions (PPIs) are responsible for a number of key physiological
processes in the living cells and underlie the pathomechanism of many diseases …

[HTML][HTML] Information-driven modeling of biomolecular complexes

CW van Noort, RV Honorato, AMJJ Bonvin - Current Opinion in Structural …, 2021 - Elsevier
Proteins play crucial roles in every cellular process by interacting with each other, nucleic
acids, metabolites, and other molecules. The resulting assemblies can be very large and …

Memdock: an α-helical membrane protein docking algorithm

N Hurwitz, D Schneidman-Duhovny… - Bioinformatics, 2016 - academic.oup.com
Motivation: A wide range of fundamental biological processes are mediated by membrane
proteins. Despite their large number and importance, less than 1% of all 3D protein …

[HTML][HTML] A membrane protein complex docking benchmark

PI Koukos, I Faro, CW van Noort… - Journal of molecular …, 2018 - Elsevier
We report the first membrane protein–protein docking benchmark consisting of 37 targets of
diverse functions and folds. The structures were chosen based on a set of parameters such …