This repository contains a tutorial for using AutoDock Vina to dock Purpurogalline to a zinc-dependent beta-lactamase, along with a reference compound. The tutorial guides users through installation, ...

In this tutorial, we explore how to generate multiple protein conformations from molecular dynamics (MD) simulations at different time points (100 ns, 200 ns, 300 ns) and use them for AutoDock Vina ...

QM/MM Tutorial Series – Part 2: Molecular Docking with CB-Dock2 In the previous post, we prepared the protein and ligand files using AutoDock Tools (ADT). Now it's time to perform the docking. One ...

ReverseDock employs a microservice architecture that enables flexible scaling. For instance, docking simulations can be distributed across multiple interconnected computers. Services are tasked with ...

Abstract 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.

Intrinsically disordered proteins (IDPs) are implicated in many human diseases and are increasingly being pursued as drug targets. Conventional structure-based drug design methods that rely on ...

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking ...

Abstract: In recent years, OpenCL has been increasingly adopted as it enables software programmers to harness the performance and power efficiency of FPGAs. Despite simplifying the FPGA programming ...