Macromolecular modeling and design in Rosetta: recent methods and frameworks
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …
in laboratories worldwide. During two decades of development by a community of …
[HTML][HTML] Protein–peptide docking: opportunities and challenges
Highlights•We provide an overview of protein-peptide docking methods and their
applications.•Peptide docking tools can be divided on template-based, local and global …
applications.•Peptide docking tools can be divided on template-based, local and global …
Harnessing protein folding neural networks for peptide–protein docking
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …
A deep-learning framework for multi-level peptide–protein interaction prediction
Peptide-protein interactions are involved in various fundamental cellular functions and their
identification is crucial for designing efficacious peptide therapeutics. Recently, a number of …
identification is crucial for designing efficacious peptide therapeutics. Recently, a number of …
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors
A Kacen, A Javitt, MP Kramer, D Morgenstern… - Nature …, 2023 - nature.com
Post-translational modification (PTM) of antigens provides an additional source of
specificities targeted by immune responses to tumors or pathogens, but identifying antigen …
specificities targeted by immune responses to tumors or pathogens, but identifying antigen …
Improving peptide-protein docking with AlphaFold-Multimer using forced sampling
I Johansson-Åkhe, B Wallner - Frontiers in bioinformatics, 2022 - frontiersin.org
Protein interactions are key in vital biological processes. In many cases, particularly in
regulation, this interaction is between a protein and a shorter peptide fragment. Such …
regulation, this interaction is between a protein and a shorter peptide fragment. Such …
Highly flexible ligand docking: Benchmarking of the DockThor program on the LEADS-PEP protein–peptide data set
Protein–peptide interactions play a crucial role in many cellular and biological functions,
which justify the increasing interest in the development of peptide-based drugs. However …
which justify the increasing interest in the development of peptide-based drugs. However …
Comprehensive evaluation of fourteen docking programs on protein–peptide complexes
A large number of protein–protein interactions (PPIs) are mediated by the interactions
between proteins and peptide segments binding partners, and therefore determination of …
between proteins and peptide segments binding partners, and therefore determination of …
From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2
The revolution brought about by AlphaFold2 opens promising perspectives to unravel the
complexity of protein-protein interaction networks. The analysis of interaction networks …
complexity of protein-protein interaction networks. The analysis of interaction networks …
Computational approaches for the design of modulators targeting protein-protein interactions
ABSTRACT Background Protein-protein interactions (PPIs) are intriguing targets for
designing novel small-molecule inhibitors. The role of PPIs in various infectious and …
designing novel small-molecule inhibitors. The role of PPIs in various infectious and …