Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

Structure‐based design of inhibitors of protein–protein interactions: mimicking peptide binding epitopes

M Pelay‐Gimeno, A Glas, O Koch… - Angewandte Chemie …, 2015 - Wiley Online Library
Protein–protein interactions (PPIs) are involved at all levels of cellular organization, thus
making the development of PPI inhibitors extremely valuable. The identification of selective …

Small-molecule inhibitors of protein-protein interactions: progressing toward the reality

MR Arkin, Y Tang, JA Wells - Chemistry & biology, 2014 - cell.com
The past 20 years have seen many advances in our understanding of protein-protein
interactions (PPIs) and how to target them with small-molecule therapeutics. In 2004, we …

Small-molecule modulators of toll-like receptors

Y Wang, S Zhang, H Li, H Wang, T Zhang… - Accounts of chemical …, 2020 - ACS Publications
Conspectus Toll-like receptors (TLRs) are the “gatekeepers” of the immune system in
humans and other animals to protect the host from invading bacteria, viruses, and other …

Modulators of protein–protein interactions

LG Milroy, TN Grossmann, S Hennig… - Chemical …, 2014 - ACS Publications
Since Hedin's characterization of trypsin and antitrypsin in 1906,(1) arguably the first
account of a regulatory protein–protein interaction (PPI), contemporary understanding of …

Peptide therapeutics: targeting the undruggable space

N Tsomaia - European journal of medicinal chemistry, 2015 - Elsevier
Rapid advancements in genomics have brought a better understanding of molecular
mechanisms for various pathologies and identified a number of highly attractive target …

Modulating protein–protein interactions: the potential of peptides

L Nevola, E Giralt - Chemical Communications, 2015 - pubs.rsc.org
Protein–protein interactions (PPIs) have emerged as important and challenging targets in
chemical biology and medicinal chemistry. The main difficulty encountered in the discovery …

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

N London, B Raveh, E Cohen, G Fathi… - Nucleic acids …, 2011 - academic.oup.com
Peptide–protein interactions are among the most prevalent and important interactions in the
cell, but a large fraction of those interactions lack detailed structural characterization. The …

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 …

Druggable protein–protein interactions–from hot spots to hot segments

N London, B Raveh, O Schueler-Furman - Current opinion in chemical …, 2013 - Elsevier
Highlights•PPIs that are dominated by a continuous epitope are amenable for inhibition.•A
significant share of PPIs contains such 'hot segments'.•Peptide-based inhibitors are obvious …