The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove binders distamycin and pentamidine. Autodock and Surflex dock daunorubicin and distamycin to their nuclei...

The Community Structure-Activity Resource (CSAR) benchmark exercise provides a unique opportunity for researchers to objectively evaluate the performance of protein-ligand docking methods. Patch-Surfer and PL-PatchSurfer, molecular surface-based methods for predicting binding ligands of proteins developed in our group, were tested on both CSAR 2013 and 2014 benchmark exercises in combination wi...

Our AutoDock-based incremental docking protocol [66], at each incremental step, explores a few rotatable bonds. A small fragment of a large ligand, with a small number of rotatable bonds, is first selected and its rotatable bonds are set active. Only the active rotatable bonds are explored in each docking operation. The fragment is docked to the protein using AutoDock [44,65] and few best-scori...

BACKGROUND Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelizat...

BACKGROUND Halogen bonding has recently come to play as a target for lead optimization in rational drug design. However, most docking program don't account for halogen bonding in their scoring functions and are not able to utilize this new approach. In this study a new and improved halogen bonding scoring function (XBSF) is presented along with its implementation in the AutoDock Vina molecular ...

Due to low cost, speed, and unmatched ability to explore large numbers of compounds, high throughput virtual screening and molecular docking engines have become widely utilized by computational scientists. It is generally accepted that docking engines, such as AutoDock, produce reliable qualitative results for ligand-macromolecular receptor binding, and molecular docking results are commonly re...