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 …
LEADS-PEP: a benchmark data set for assessment of peptide docking performance
AS Hauser, B Windshügel - Journal of Chemical Information and …, 2016 - ACS Publications
With increasing interest in peptide-based therapeutics also the application of computational
approaches such as peptide docking has gained more and more attention. In order to …
approaches such as peptide docking has gained more and more attention. In order to …
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 …
MDockPeP: An ab‐initio protein–peptide docking server
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 complex structure is a key to understand the mechanisms underlying protein …
Hierarchical flexible peptide docking by conformer generation and ensemble docking of peptides
Given the importance of peptide-mediated protein interactions in cellular processes, protein–
peptide docking has received increasing attention. Here, we have developed a H ierarchical …
peptide docking has received increasing attention. Here, we have developed a H ierarchical …
Improved docking of polypeptides with Glide
I Tubert-Brohman, W Sherman… - Journal of chemical …, 2013 - ACS Publications
Predicting the binding mode of flexible polypeptides to proteins is an important task that falls
outside the domain of applicability of most small molecule and protein–protein docking tools …
outside the domain of applicability of most small molecule and protein–protein docking tools …
A unified conformational selection and induced fit approach to protein-peptide docking
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 …
components in nearly 40% of all macromolecular interactions, and are often associated with …
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
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 …
characterization, though challenging, is important for the discovery of new drugs. The CABS …
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 …
CABS-dock standalone: a toolbox for flexible protein–peptide docking
M Kurcinski, M Pawel Ciemny, T Oleniecki… - …, 2019 - academic.oup.com
CABS-dock standalone is a multiplatform Python package for protein–peptide docking with
backbone flexibility. The main feature of the CABS-dock method is its ability to simulate …
backbone flexibility. The main feature of the CABS-dock method is its ability to simulate …