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 …

[HTML][HTML] 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 …

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 …

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 …

[HTML][HTML] 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 …

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 …

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

M Kurcinski, M Jamroz, M Blaszczyk… - Nucleic acids …, 2015 - academic.oup.com
Protein–peptide interactions play a key role in cell functions. Their structural
characterization, though challenging, is important for the discovery of new drugs. The CABS …

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

H Lee, L Heo, MS Lee, C Seok - Nucleic acids research, 2015 - academic.oup.com
Protein–peptide interactions are involved in a wide range of biological processes and are
attractive targets for therapeutic purposes because of their small interfaces. Therefore …

[HTML][HTML] A unified conformational selection and induced fit approach to protein-peptide docking

M Trellet, ASJ Melquiond, AMJJ Bonvin - PloS one, 2013 - journals.plos.org
Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural
components in nearly 40% of all macromolecular interactions, and are often associated with …

[HTML][HTML] 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 …