UNLABELLED A protein-protein docking decoy set is built for the Dockground unbound benchmark set. The GRAMM-X docking scan was used to generate 100 non-native and at least one near-native match per complex for 61 complexes. The set is a publicly available resource for the development of scoring functions and knowledge-based potentials for protein docking methodologies. AVAILABILITY The decoys...

In recent years, the importance of considering induced fit effects in molecular docking calculations has been widely recognised in the molecular modelling community. While small-scale protein side-chain movements are now accounted for in many state-of-the-art docking strategies, the explicit modelling of large-scale protein motions such as loop movements in kinase domains is still a challenging...

Few methods use molecular dynamics simulations based on atomically detailed force fields to study the proteinligand docking process because they are considered too time demanding despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics simulations which has a highly flexible computational granularity. We compare the accuracy and the time required with wel...

Wnts are the major ligands responsible for activating Wnt signaling pathway through binding to Frizzled proteins (Fzd) as the receptors. Among these ligands, Wnt2 plays the main role in the tumorigenesis of several human cancers especially colorectal cancer (CRC). Therefore, it can be considered as a potential drug target.The aim of this study was to identify potential drug candidates ...

Multitarget agents have been extensively explored for solving limited efficacies, poor safety, and resistant profiles of an individual target. Theoretical approaches for searching and designing multitarget agents are critically useful. Here, the performance of molecular docking to search dual-target inhibitors for four kinase pairs (CDK2-GSK3B, EGFR-Src, Lck-Src, and Lck-VEGFR2) was assessed. F...