SeamDock: an interactive and collaborative online docking resource to assist small compound molecular docking

S Murail, SJ De Vries, J Rey, G Moroy… - Frontiers in Molecular …, 2021 - frontiersin.org
In silico assessment of protein receptor interactions with small ligands is now part of the
standard pipeline for drug discovery, and numerous tools and protocols have been …

Dockey: a modern integrated tool for large-scale molecular docking and virtual screening

L Du, C Geng, Q Zeng, T Huang, J Tang… - Briefings in …, 2023 - academic.oup.com
Molecular docking is a structure-based and computer-aided drug design approach that
plays a pivotal role in drug discovery and pharmaceutical research. AutoDock is the most …

DockingPie: a consensus docking plugin for PyMOL

S Rosignoli, A Paiardini - Bioinformatics, 2022 - academic.oup.com
Motivation The primary strategy for predicting the binding mode of small molecules to their
receptors and for performing receptor-based virtual screening studies is protein–ligand …

BP-Dock: a flexible docking scheme for exploring protein–ligand interactions based on unbound structures

A Bolia, ZN Gerek, SB Ozkan - Journal of chemical information …, 2014 - ACS Publications
Molecular docking serves as an important tool in modeling protein–ligand interactions.
However, it is still challenging to incorporate overall receptor flexibility, especially backbone …

DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina

E Di Muzio, D Toti, F Polticelli - Journal of Computer-Aided Molecular …, 2017 - Springer
Molecular docking is a powerful technique that helps uncover the structural and energetic
bases of the interaction between macromolecules and substrates, endogenous and …

PacDOCK: A Web server for positional distance-based and interaction-based analysis of docking results

J Carbone, A Ghidini, A Romano, L Gentilucci… - Molecules, 2022 - mdpi.com
Molecular docking is a key method for structure-based drug design used to predict the
conformations assumed by small drug-like ligands when bound to their target. However, the …

istar: A web platform for large-scale protein-ligand docking

H Li, KS Leung, PJ Ballester, MH Wong - PLoS One, 2014 - journals.plos.org
Protein-ligand docking is a key computational method in the design of starting points for the
drug discovery process. We are motivated by the desire to automate large-scale docking …

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking

G Bottegoni, I Kufareva, M Totrov… - Journal of medicinal …, 2009 - ACS Publications
Many available methods aimed at incorporating the receptor flexibility in ligand docking are
computationally expensive, require a high level of user intervention, and were tested only on …

InVADo: interactive visual analysis of molecular docking data

M Schäfer, N Brich, J Byška… - … on Visualization and …, 2023 - ieeexplore.ieee.org
Molecular docking is a key technique in various fields like structural biology, medicinal
chemistry, and biotechnology. It is widely used for virtual screening during drug discovery …

DockThor-VS: A Free Platform for Receptor-Ligand Virtual Screening

IA Guedes, MMP da Silva, M Galheigo… - Journal of Molecular …, 2024 - Elsevier
The DockThor-VS platform (https://dockthor. lncc. br/v2/) is a free protein–ligand docking
server conceptualized to facilitate and assist drug discovery projects to perform docking …