Molecular dynamics simulations in drug discovery and pharmaceutical development
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …
development process. In this review, we give a broad overview of the current application …
Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm
Protein–peptide interactions are crucial in many cellular functions. Therefore, determining
the structure of protein–peptide complexes is important for understanding the molecular …
the structure of protein–peptide complexes is important for understanding the molecular …
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex
A Lamiable, P Thévenet, J Rey, M Vavrusa… - Nucleic acids …, 2016 - academic.oup.com
Abstract Structure determination of linear peptides of 5–50 amino acids in aqueous solution
and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel …
and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel …
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 …
[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 …
Benchmarking of different molecular docking methods for protein-peptide docking
Background Molecular docking studies on protein-peptide interactions are a challenging
and time-consuming task because peptides are generally more flexible than proteins and …
and time-consuming task because peptides are generally more flexible than proteins and …
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding
Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …
play an important role in cellular signaling. However, it is challenging to simulate both …
AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes
Motivation Protein–peptide interactions mediate a wide variety of cellular and biological
functions. Methods for predicting these interactions have garnered a lot of interest over the …
functions. Methods for predicting these interactions have garnered a lot of interest over the …
Interfering peptides targeting protein–protein interactions: the next generation of drugs?
H Bruzzoni-Giovanelli, V Alezra, N Wolff, CZ Dong… - Drug Discovery …, 2018 - Elsevier
Highlights•Structure-based strategies allow more-specific targeting of protein–protein
interactions (PPIs).•Interfering peptides (IPs) become a promising alternative to small …
interactions (PPIs).•Interfering peptides (IPs) become a promising alternative to small …