De novo protein design, a retrospective

IV Korendovych, WF DeGrado - Quarterly reviews of biophysics, 2020 - cambridge.org
Proteins are molecular machines whose function depends on their ability to achieve
complex folds with precisely defined structural and dynamic properties. The rational design …

Drugging membrane protein interactions

H Yin, AD Flynn - Annual review of biomedical engineering, 2016 - annualreviews.org
The majority of therapeutics target membrane proteins, accessible on the surface of cells, to
alter cellular signaling. Cells use membrane proteins to transduce signals into cells …

Spatial arrangement of proteins in planar and curved membranes by PPM 3.0

AL Lomize, SC Todd, ID Pogozheva - Protein Science, 2022 - Wiley Online Library
Cellular protrusions, invaginations, and many intracellular organelles have strongly curved
membrane regions. Transmembrane and peripheral membrane proteins that induce, sense …

OPM database and PPM web server: resources for positioning of proteins in membranes

MA Lomize, ID Pogozheva, H Joo… - Nucleic acids …, 2012 - academic.oup.com
Abstract The Orientations of Proteins in Membranes (OPM) database is a curated web
resource that provides spatial positions of membrane-bound peptides and proteins of known …

Molecular code for transmembrane-helix recognition by the Sec61 translocon

T Hessa, NM Meindl-Beinker, A Bernsel, H Kim, Y Sato… - Nature, 2007 - nature.com
Transmembrane α-helices in integral membrane proteins are recognized co-translationally
and inserted into the membrane of the endoplasmic reticulum by the Sec61 translocon. A full …

De novo design of a transmembrane Zn2+-transporting four-helix bundle

NH Joh, T Wang, MP Bhate, R Acharya, Y Wu, M Grabe… - Science, 2014 - science.org
The design of functional membrane proteins from first principles represents a grand
challenge in chemistry and structural biology. Here, we report the design of a membrane …

HAPPENN is a novel tool for hemolytic activity prediction for therapeutic peptides which employs neural networks

PB Timmons, CM Hewage - Scientific reports, 2020 - nature.com
The growing prevalence of resistance to antibiotics motivates the search for new
antibacterial agents. Antimicrobial peptides are a diverse class of well-studied membrane …

[Књига][B] Introduction to proteins: structure, function, and motion

A Kessel, N Ben-Tal - 2018 - taylorfrancis.com
Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …

modlAMP: Python for antimicrobial peptides

AT Müller, G Gabernet, JA Hiss, G Schneider - Bioinformatics, 2017 - academic.oup.com
We have implemented the mo lecular d esign l aboratory'sa nti m icrobial p eptides package
(modlAMP), a Python-based software package for the design, classification and visual …

De novo-designed transmembrane proteins bind and regulate a cytokine receptor

M Mravic, L He, HT Kratochvil, H Hu, SE Nick… - Nature Chemical …, 2024 - nature.com
Transmembrane (TM) domains as simple as a single span can perform complex biological
functions using entirely lipid-embedded chemical features. Computational design has the …