Dockey: a modern integrated tool for large-scale molecular docking and virtual screening
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 …
plays a pivotal role in drug discovery and pharmaceutical research. AutoDock is the most …
[HTML][HTML] istar: A web platform for large-scale protein-ligand docking
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 …
drug discovery process. We are motivated by the desire to automate large-scale docking …
The art and science of molecular docking
Molecular docking has become an essential part of a structural biologist's and medicinal
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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 …
AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared …
Automated docking screens: a feasibility study
JJ Irwin, BK Shoichet, MM Mysinger… - Journal of medicinal …, 2009 - ACS Publications
Molecular docking is the most practical approach to leverage protein structure for ligand
discovery, but the technique retains important liabilities that make it challenging to deploy on …
discovery, but the technique retains important liabilities that make it challenging to deploy on …
Blind docking of 260 protein–ligand complexes with EADock 2.0
A Grosdidier, V Zoete… - Journal of computational …, 2009 - Wiley Online Library
Molecular docking softwares are one of the important tools of modern drug development
pipelines. The promising achievements of the last 10 years emphasize the need for further …
pipelines. The promising achievements of the last 10 years emphasize the need for further …
[HTML][HTML] Can we still trust docking results? An extension of the applicability of DockBench on PDBbind database
The number of entries in the Protein Data Bank (PDB) has doubled in the last decade, and it
has increased tenfold in the last twenty years. The availability of an ever-growing number of …
has increased tenfold in the last twenty years. The availability of an ever-growing number of …
[HTML][HTML] DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0
Background Small-molecule docking is an important tool in studying receptor-ligand
interactions and in identifying potential drug candidates. Previously, we developed a …
interactions and in identifying potential drug candidates. Previously, we developed a …
ProBiS-Dock: A hybrid multitemplate homology flexible docking algorithm enabled by protein binding site comparison
The protein data bank (PDB) is a rich source of protein ligand structures, but ligands are not
explicitly used in current docking algorithms. We have developed ProBiS-Dock, a docking …
explicitly used in current docking algorithms. We have developed ProBiS-Dock, a docking …
DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large‐scale docking
TE Balius, YS Tan, M Chakrabarti - Journal of Computational …, 2024 - Wiley Online Library
To allow DOCK 6 access to unprecedented chemical space for screening billions of small
molecules, we have implemented features from DOCK 3.7 into DOCK 6, including a search …
molecules, we have implemented features from DOCK 3.7 into DOCK 6, including a search …