AutoDock

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina. AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.


References in zbMATH (referenced in 34 articles )

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  1. Rayhan, Farshid; Ahmed, Sajid; Md Farid, Dewan; Dehzangi, Abdollah; Shatabda, Swakkhar: CFSBoost: cumulative feature subspace boosting for drug-target interaction prediction (2019)
  2. Fu, Yi; Chen, Zhiguo; Sun, Jun: Random drift particle swarm optimisation algorithm for highly flexible protein-ligand docking (2018)
  3. Janaina Cruz Pereira, Ernesto Raul Caffarena, Cicero dos Santos: Boosting Docking-based Virtual Screening with Deep Learning (2016) arXiv
  4. Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon: Using persistent homology and dynamical distances to analyze protein binding (2016)
  5. Fatemi, Mohammad H.; Heidari, Afsane; Gharaghani, Sajjad: QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors (2015)
  6. Lampariello, Francesco; Liuzzi, Giampaolo: Global optimization of protein-peptide docking by a filling function method (2015)
  7. Qi, Hang; Ma, Shoufeng; Jia, Ning; Wang, Guangchao: Experiments on individual strategy updating in iterated snowdrift game under random rematching (2015)
  8. Ellenberger, Sabrina; Schuster, Stefan; Wöstemeyer, Johannes: Correlation between sequence, structure and function for trisporoid processing proteins in the model zygomycete \textitMucormucedo (2013)
  9. Al-Bluwi, Ibrahim; Siméon, Thierry; Cortés, Juan: Motion planning algorithms for molecular simulations: a survey (2012)
  10. Yasser Gonzalez-Fernandez, Marta Soto: copulaedas: An R Package for Estimation of Distribution Algorithms Based on Copulas (2012) arXiv
  11. Netto, Marco A. S.; Vecchiola, Christian; Kirley, Michael; Varela, Carlos A.; Buyya, Rajkumar: Use of run time predictions for automatic co-allocation of multi-cluster resources for iterative parallel applications (2011) ioport
  12. Aita, Takuyo; Nishigaki, Koichi; Husimi, Yuzuru: Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential (2010)
  13. Boisson, Jean-Charles; Jourdan, Laetitia; Talbi, El-Ghazali; Horvath, Dragos: Single- and multi-objective cooperation for the flexible docking problem (2010) ioport
  14. Durrant, Jacob D.; McCammon, J. Andrew: Potential drug-like inhibitors of group 1 influenza neuraminidase identified through computer-aided drug design (2010)
  15. Kim, Chong-Min; Won, Chung-In; Kim, Jae-Kwan; Ryu, Joonghyun; Bhak, Jong; Kim, Deok-Soo: Protein-ligand docking based on beta-shape (2010)
  16. Xie, Zhong-Ru; Hwang, Ming-Jing: An interaction-motif-based scoring function for protein-ligand docking (2010) ioport
  17. Li, Honglin; Zhang, Hailei; Zheng, Mingyue; Luo, Jie; Kang, Ling; Liu, Xiaofeng; Wang, Xicheng; Jiang, Hualiang: An effective docking strategy for virtual screening based on multi-objective optimization algorithm (2009) ioport
  18. Lise, Stefano; Archambeau, Cédric; Pontil, Massimiliano; Jones, David T.: Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods (2009) ioport
  19. Liu, Xiaofeng; Bai, Fang; Ouyang, Sisheng; Wang, Xicheng; Li, Honglin; Jiang, Hualiang: Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation (2009) ioport
  20. Morris, Garrett M.; Huey, Ruth; Lindstrom, William; Sanner, Michel F.; Belew, Richard K.; Goodsell, David S.; Olson, Arthur J.: Autodock4 and autodocktools4: automated docking with selective receptor flexibility (2009) ioport

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