In recent years, much attention has been devoted to the protein-peptide docking problem in which docking of a flexible peptide with a given protein is sought. In this work, we present a docking algorithm which is based on the use of a filling function method for continuous global optimization...
In recent years, a variety of approaches have been developed for ‘protein–peptide docking’, that is, predicting the structure of the protein–peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and...
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 interactions and is critical for peptide therapeutic development. We present a user-friendly protein-peptide docking ...
FRODOCK: A new approach for fast rotational protein-protein docking Prediction of protein-protein complexes from the coordinates of their unbound components usually starts by generating many potential predictions from a rig... José Ignacio Garzonsup/sup, José Ramón Lopéz-Blancosup/sup, Carles Pons...
Protein folding and peptide docking: A molecular modeling and global optimization approachProtein folding and peptide docking: A molecular modeling and global optimization approachPractical, Theoretical or Mathematical/ chemical engineering computingfree energyoptimisation...
Therefore, we propose a new scoring function, dMM-PBSA, to be used together with the built-in HADDOCK score in the context of protein-peptide docking simulations. 展开 关键词: MM-PBSA scoring function binding free energies haddock protein-peptide interaction ...
Modelling peptide-protein complexes: docking, simulations and machine learning doi:10.1017/qrd.2022.14QRB DiscoveryMondal, ArupLiwei ChangPerez, Alberto
protein–peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, HPEPDOCK considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program. For blind global peptide docking, HPEPDOCK obtained a ...
A flexible protein−peptide docking method has been designed to consider not only ligand flexibility but also the flexibility of the protein. The method is based on a Monte Carlo annealing process. Simulations with a distance root-mean-square (dRMS) virtual energy function revealed that the flexi...
Harnessing protein folding neural networks for peptide–protein docking Article Open access 10 January 2022 Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations Article Open access 21 February 2024 Introduction Fusing compact protein binders to vari...