Fast, accurate, and reliable molecular docking with QuickVina 2
By Amr Alhossary, Stephanus Daniel Handoko, Yuguang Mu, Chee Keong Kwoh. 2015
387 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Computational Theory and Mathematics
- Tommi S. Jaakkola
- Regina Barzilay
- Shitong Luo
- Marinka Zitnik
- Tianfan Fu
- Jure Leskovec
- Jimeng Sun
- Hannes Stärk
In Molecular Biology
- Tommi S. Jaakkola
- Regina Barzilay
- Marinka Zitnik
- Jure Leskovec
- Shitong Luo
- Hannes Stärk
- Cao Xiao
- Kexin Huang
Citations in the corpus
- DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking (2022, methodology): “QuickVina-W [15] extends the speed-optimized QuickVina 2 [25] for blind docking.”
- Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration (2017, methodology): “• For the RMSD measure, a prediction was considered to be successful if the RMSD of the predicted pose (as calculated in 4,8,9 ) with respect to the experimental structure is less than 2 Å.”
- A 3D Generative Model for Structure-Based Drug Design (2022, methodology): “(3) Binding Affinity : We use Vina [1, 33] to compute the the generated molecules’ binding affinity to the target.”
- Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development (2021, methodology): “…docking where we adopted a Python wrapper from pyscreener (Graff et al. 2020) to allow easy access to various docking software, including AutoDock Vina (Trott & Olson 2010), smina (Koes et al. 2013), Quick Vina 2 (Alhossary et al. 2015), PSOVina (Ng et al. 2015), and DOCK6 (Allen et al. 2015).”
- A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia (2022, methodology): “To evaluate the hit compounds obtained from DrugBank and to calculate their interaction and binding posture in the active site of target proteins, the molecular docking method was carried out through QuickVina 2 [32].”
- Structure-based drug design with equivariant diffusion models (2022, positive): “Docking scores are obtained after local minimization with an empirical force field using the GNINA implementation 58 or, if specified, after redocking with QuickVina2 64 .”