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.

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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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