HDACs are important anticancer drug targets, and their study is currently being actively pursued. A series of HDAC inhibitors were docked to the homology models to understand the similarities and differences between the binding modes, docking analysis was applied to clarify the binding modes between the ligands and the receptor HDAC. The docking studies of some newly designed hydroxamate analog...

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...

Intrinsic flexibility of DNA has hampered the development of efficient protein-DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731-1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimiza...

Computational prediction of the 3D structures of molecular interactions is a challenging area, often requiring significant computational resources to produce structural predictions with atomic-level accuracy. This can be particularly burdensome when modeling large sets of interactions, macromolecular assemblies, or interactions between flexible proteins. We previously developed a protein dockin...

The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a mol...

INTRODUCTION Protein-ligand interactions play key roles in various metabolic pathways, and the proteins involved in these interactions represent major targets for drug discovery. Molecular docking is widely used to predict the structure of protein-ligand complexes, and protein flexibility stands out as one of the most important and challenging issues for binding mode prediction. Various docking...

The expression of heat shock protein 27 (Hsp27) as a chaperone protein, is increased in response to various stress stimuli such as anticancer chemotherapy. This phenomenon can lead to survive of the cells and causes drug resistance. In this study, a series of methanesulfonamide derivatives as dual Hsp27 and tubulin inhibitors in the treatment of cancer were applied to quantitative structure–act...

Docking to the plasma membrane prepares vesicles for rapid release. Here, we describe a mechanism for dense core vesicle docking in neurons. In Caenorhabditis elegans motor neurons, dense core vesicles dock at the plasma membrane but are excluded from active zones at synapses. We have found that the calcium-activated protein for secretion (CAPS) protein is required for dense core vesicle dockin...

introduction:  stereotactic  radiosurgery  is  a  technique  for  the  treatment  of  intracranial  lesions  with  highly  collimated  x-ray  beam.  linac-based  radiosurgery  is  currently  performed  by  two  techniques:  couch or pedestal mounted. in the first technique, a device is required to affix patient's head to a couch  and  moreover  to  translate  it  accurately.  structure  of...