Search results for "AutoDock"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
75	Emrah Atilgan, Jianjun Hu	Efficient protein-ligand docking using sustainable evolutionary algorithm.	GECCO	2010	DBLP DOI BibTeX RDF	HFC, autodock, protein docking, sustainable evolutionary algorithms, genetic algorithm
69	Li Wang 0009, Zi-jun Weng, Yi Liang, Yong Wang, Zheng Zhang, Ruihua Di	Design and Implementation of Parallel Lamarckian Genetic Algorithm for Automated Docking of Molecules.	HPCC	2008	DBLP DOI BibTeX RDF
69	Rafael Ördög, Vince Grolmusz	Evaluating Genetic Algorithms in Protein-Ligand Docking.	ISBRA	2008	DBLP DOI BibTeX RDF
51	Thomas Gaillard	Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark.	J. Chem. Inf. Model.	2018	DBLP DOI BibTeX RDF
51	Mathew R. Koebel, Grant Schmadeke, Richard G. Posner, Suman Sirimulla	AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina.	J. Cheminformatics	2016	DBLP DOI BibTeX RDF
46	Giovanni Cincilla, David Vidal, Miquel Pons	An improved scoring function for suboptimal polar ligand complexes.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Solvation, Drug design, Virtual screening, Docking, Scoring function
46	Bo-Fu Liu, Hung-Ming Chen, Hui-Ling Huang, Shiow-Fen Hwang, Shinn-Ying Ho	Flexible protein-ligand docking using particle swarm optimization.	Congress on Evolutionary Computation	2005	DBLP DOI BibTeX RDF
29	Imre Pechan, Béla Fehér	Molecular Docking on FPGA and GPU Platforms.	FPL	2011	DBLP DOI BibTeX RDF	FPGA vs, AutoDock, bioinformatics, GPU, hardware acceleration, molecular docking
29	Xiaohui Wei, Lixian Xi, Hongliang Li, Haibin Wang, Wilfred W. Li, Jingyuan Ren	A Case of Meta-scheduling for Biological Researches in Cloud Environment.	FCST	2010	DBLP DOI BibTeX RDF	CSF4, OPAL, Autodock, Cloud computing
29	Karina S. Machado, Evelyn K. Schroeder, Duncan D. Ruiz, Ana Wink, Osmar Norberto de Souza	Extracting Information from Flexible Receptor-Flexible Ligand Docking Experiments.	BSB	2008	DBLP DOI BibTeX RDF	AutoDock, Data Mining, Molecular Docking, Molecular Dynamics Simulation, WEKA
26	Junkai Ji, Jin Zhou, Zhangfan Yang, Qiuzhen Lin, Carlos A. Coello Coello	AutoDock Koto: A Gradient Boosting Differential Evolution for Molecular Docking.	IEEE Trans. Evol. Comput.	2023	DBLP DOI BibTeX RDF
26	Xingxing Zhou, Ming Ling, Qingde Lin, Shidi Tang, Jiansheng Wu, Haifeng Hu 0004	Effectiveness Analysis of Multiple Initial States Simulated Annealing Algorithm, a Case Study on the Molecular Docking Tool AutoDock Vina.	IEEE ACM Trans. Comput. Biol. Bioinform.	2023	DBLP DOI BibTeX RDF
26	Ji Ding, Shidi Tang, Zheming Mei, Lingyue Wang, Qinqin Huang, Haifeng Hu 0004, Ming Ling, Jiansheng Wu	Vina-GPU 2.0: Further Accelerating AutoDock Vina and Its Derivatives with Graphics Processing Units.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
26	Gabin Schieffer, Ivy Bo Peng	Accelerating Drug Discovery in AutoDock-GPU with Tensor Cores.	Euro-Par	2023	DBLP DOI BibTeX RDF
26	Zhangfan Yang, Kun Cao, Junkai Ji, Zexuan Zhu, Jianqiang Li 0001	Adopting Autodock Koto for Virtual Screening of COVID-19.	ICIC (3)	2023	DBLP DOI BibTeX RDF
26	T. Ngoc Han Pham, Trung Hai Nguyen, Nguyen Minh Tam, Thien Y. Vu, Nhat Truong Pham, Nguyen Truong Huy, Binh Khanh Mai, Nguyen Thanh Tung, Minh Quan Pham, Van V. Vu, Son Tung Ngo 0002	Improving ligand-ranking of AutoDock Vina by changing the empirical parameters.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
26	Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch 0001, Scott LeGrand, Stefano Forli	Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking.	Parallel Comput.	2022	DBLP DOI BibTeX RDF
26	Jérôme Eberhardt, Diogo Santos-Martins, Andreas F. Tillack, Stefano Forli	AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
26	Zhuoran Liu 0002, Dingde Jiang, Changsheng Zhang 0001, Haitong Zhao, Qidong Zhao, Bin Zhang 0001	A Novel Fireworks Algorithm for the Protein-Ligand Docking on the AutoDock.	Mob. Networks Appl.	2021	DBLP DOI BibTeX RDF
26	Maria Kadukova, Vladimir Chupin, Sergei Grudinin	Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4.	J. Comput. Aided Mol. Des.	2020	DBLP DOI BibTeX RDF
26	Enade P. Istyastono, Muhammad Radifar, Nunung Yuniarti, Vivitri D. Prasasty, Sudi Mungkasi	PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS.	J. Chem. Inf. Model.	2020	DBLP DOI BibTeX RDF
26	Nguyen Thanh Nguyen, Trung Hai Nguyen, T. Ngoc Han Pham, Nguyen Truong Huy, Mai Van Bay, Minh Quan Pham, Pham Cam Nam, Van V. Vu, Son Tung Ngo 0002	Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity.	J. Chem. Inf. Model.	2020	DBLP DOI BibTeX RDF
26	Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, Jacob D. Durrant, Yann Ponty	Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser.	Bioinform.	2020	DBLP DOI BibTeX RDF
26	Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch 0001, Stefano Forli	Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking.	PDP	2020	DBLP DOI BibTeX RDF
26	D. Tomic, Davor Davidovic, V. Jandel, J. Mesaric, Karolj Skala, Tomislav Lipic	Drug screening with the Autodock Vina on a set of kinases without experimentally established structures.	MIPRO	2020	DBLP DOI BibTeX RDF
26	Yuqi Zhang, Stefano Forli, Anna Omelchenko, Michel F. Sanner	AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.	J. Comput. Chem.	2019	DBLP DOI BibTeX RDF
26	Lea El-Khoury, Diogo Santos-Martins, Sukanya Sasmal, Jérôme Eberhardt, Giulia Bianco, Francesca Alessandra Ambrosio, Leonardo Solis-Vasquez, Andreas Koch 0001, Stefano Forli, David L. Mobley	Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4.	J. Comput. Aided Mol. Des.	2019	DBLP DOI BibTeX RDF
26	Diogo Santos-Martins, Jérôme Eberhardt, Giulia Bianco, Leonardo Solis-Vasquez, Francesca Alessandra Ambrosio, Andreas Koch 0001, Stefano Forli	D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU.	J. Comput. Aided Mol. Des.	2019	DBLP DOI BibTeX RDF
26	Yuqi Zhang, Michel F. Sanner	AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes.	Bioinform.	2019	DBLP DOI BibTeX RDF
26	Juan Pablo Arcon, Carlos P. Modenutti, Demian Avendaño, Elias D. López, Lucas A. Defelipe, Francesca Alessandra Ambrosio, Adrian Gustavo Turjanski, Stefano Forli, Marcelo A. Marti	AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.	Bioinform.	2019	DBLP DOI BibTeX RDF
26	Zhuoran Liu 0002, Changsheng Zhang 0001, Qidong Zhao, Bin Zhang 0001, Wenjuan Sun	Comparative Study of Evolutionary Algorithms for Protein-Ligand Docking Problem on the AutoDock.	SimuTools	2019	DBLP DOI BibTeX RDF
26	Maria Kadukova, Sergei Grudinin	Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.	J. Comput. Aided Mol. Des.	2018	DBLP DOI BibTeX RDF
26	Hojjat Rakhshani, Lhassane Idoumghar, Julien Lepagnot, Mathieu Brévilliers, Edward C. Keedwell	Automatic hyperparameter selection in Autodock.	CoRR	2018	DBLP BibTeX RDF
26	G. W. McElfresh, Christos Deligkaris	A vibrational entropy term for DNA docking with autodock.	Comput. Biol. Chem.	2018	DBLP DOI BibTeX RDF
26	A. Samdani, Umashankar Vetrivel	POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening.	Comput. Biol. Chem.	2018	DBLP DOI BibTeX RDF
26	Mark S. Hisle, Maxwell S. Meier, David M. Toth	Accelerating AutoDock Vina with Containerization.	PEARC	2018	DBLP DOI BibTeX RDF
26	Hojjat Rakhshani, Lhassane Idoumghar, Julien Lepagnot, Mathieu Brévilliers, Edward C. Keedwell	Automatic hyperparameter selection in Autodock.	BIBM	2018	DBLP DOI BibTeX RDF
26	Elena Di Muzio, Daniele Toti, Fabio Polticelli	DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina.	J. Comput. Aided Mol. Des.	2017	DBLP DOI BibTeX RDF
26	Carlos García-Pérez, Rafael Peláez, Roberto Therón, José Luis López-Pérez	JADOPPT: java based AutoDock preparing and processing tool.	Bioinform.	2017	DBLP DOI BibTeX RDF
26	Génesis Varela-Salinas, Carlos Armando García-Pérez, Rafael Peláez, Adolfo J. Rodríguez	Visual Clustering Approach for Docking Results from Vina and AutoDock.	HAIS	2017	DBLP DOI BibTeX RDF
26	Mohammad Mahdi Jaghoori, Boris Bleijlevens, Sílvia Delgado Olabarriaga	1001 Ways to run AutoDock Vina for virtual screening.	J. Comput. Aided Mol. Des.	2016	DBLP DOI BibTeX RDF
26	Lang Yu, Zhongzhi Luan, Xiangzheng Sun, Zhe Wang, Hailong Yang	VinaSC: Scalable Autodock Vina with fine-grained scheduling on heterogeneous platform.	BIBM	2016	DBLP DOI BibTeX RDF
26	Robert Rentzsch, Bernhard Y. Renard	Docking small peptides remains a great challenge: an assessment using AutoDock Vina.	Briefings Bioinform.	2015	DBLP DOI BibTeX RDF
26	Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson	Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.	J. Comput. Aided Mol. Des.	2014	DBLP DOI BibTeX RDF
26	Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson	AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins.	J. Chem. Inf. Model.	2014	DBLP DOI BibTeX RDF
26	Muhammad Hilman, Heru Suhartanto, Arry Yanuar	Performance Analysis of Embarassingly Parallel Application on Cluster Computer Environment: A Case Study of Virtual Screening with Autodock Vina 1.1 on Hastinapura Cluster.	CoRR	2013	DBLP BibTeX RDF
26	Stephanus Daniel Handoko, Xuchang Ouyang, Chinh Tran To Su, Chee Keong Kwoh 0001, Yew-Soon Ong	QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization.	IEEE ACM Trans. Comput. Biol. Bioinform.	2012	DBLP DOI BibTeX RDF
26	Stephanus Daniel Handoko, Xuchang Ouyang, Chinh Tran To Su, Chee Keong Kwoh 0001, Yew-Soon Ong	Erratum to "QuickVina: Accelerating AutoDock Vina Using Gradient-Based Heuristics for Global Optimization".	IEEE ACM Trans. Comput. Biol. Bioinform.	2012	DBLP DOI BibTeX RDF
26	M. Naresh Babu, R. Bhramaramba, Allam Appa Rao	Structure based drug design studies on urokinase plasminogen activator inhibitors using AutoDock.	CCSEIT	2012	DBLP DOI BibTeX RDF
26	Andrew P. Norgan, Paul K. Coffman, Jean-Pierre A. Kocher, David J. Katzmann, Carlos P. Sosa	Multilevel Parallelization of AutoDock 4.2.	J. Cheminformatics	2011	DBLP DOI BibTeX RDF
26	Oleg Trott, Arthur J. Olson	AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.	J. Comput. Chem.	2010	DBLP DOI BibTeX RDF
26	Hamed I. Ali, Takayuki Fujita, Eiichi Akaho, Tomohisa Nagamatsu	A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors.	J. Comput. Aided Mol. Des.	2010	DBLP DOI BibTeX RDF
26	Daniel Seeliger, Bert L. de Groot	Ligand docking and binding site analysis with PyMOL and Autodock/Vina.	J. Comput. Aided Mol. Des.	2010	DBLP DOI BibTeX RDF
26	Giulio Vistoli, Alessandro Pedretti, Angelica Mazzolari, Bernard Testa	Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0.	J. Comput. Aided Mol. Des.	2010	DBLP DOI BibTeX RDF
26	Nikita D. Prakhov, Alexander L. Chernorudskiy, Murat R. Gainullin	VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters.	Bioinform.	2010	DBLP DOI BibTeX RDF
26	Sarnath Kannan, Raghavendra Ganji	Porting Autodock to CUDA.	IEEE Congress on Evolutionary Computation	2010	DBLP DOI BibTeX RDF
26	Rohit Tiwari, Kiran Mahasenan, Ryan E. Pavlovicz, Chenglong Li, Werner Tjarks	Carborane Clusters in Computational Drug Design: A Comparative Docking Evaluation Using AutoDock, FlexX, Glide, and Surflex.	J. Chem. Inf. Model.	2009	DBLP DOI BibTeX RDF
26	Janos Nadas, Chenglong Li, Peng George Wang	Computational Structure Activity Relationship Studies on the CD1d/Glycolipid/TCR Complex Using AMBER and AUTODOCK.	J. Chem. Inf. Model.	2009	DBLP DOI BibTeX RDF
26	Zsolt Bikádi, Eszter Hazai	Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock.	J. Cheminformatics	2009	DBLP DOI BibTeX RDF
26	Shuxing Zhang, Kamal Kumar 0002, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman	DOVIS: an implementation for high-throughput virtual screening using AutoDock.	BMC Bioinform.	2008	DBLP DOI BibTeX RDF
26	Patrick A. Holt, Jonathan B. Chaires, John O. Trent	Molecular Docking of Intercalators and Groove-Binders to Nucleic Acids Using Autodock and Surflex.	J. Chem. Inf. Model.	2008	DBLP DOI BibTeX RDF
26	Stefano Forli, Maurizio Botta	Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems.	J. Chem. Inf. Model.	2007	DBLP DOI BibTeX RDF
26	Montserrat Vaqué, Anna Arola, Carles Aliagas, Gerard Pujadas	BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock.	Bioinform.	2006	DBLP DOI BibTeX RDF
26	Oleksandr V. Buzko, Anthony C. Bishop, Kevan M. Shokat	Modified AutoDock for accurate docking of protein kinase inhibitors.	J. Comput. Aided Mol. Des.	2002	DBLP DOI BibTeX RDF
26	Michael Thormann, Hans-Jörg Hofmann	Docking experiences, AutoDock - a Case Study.	German Conference on Bioinformatics	1998	DBLP BibTeX RDF
26	Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson	Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4.	J. Comput. Aided Mol. Des.	1996	DBLP DOI BibTeX RDF
23	Hongwei Zhou, Wai-Ping Lai, Zhiqiang Zhang, Wai-Kee Li, Hon-Yeung Cheung	Computational study on the molecular inclusion of andrographolide by cyclodextrin.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Andrographolide, Cyclodextrin, Inclusion complex, Hydrogen bond
23	Zhaohui Ding, Xiaohui Wei, Yuan Luo, Da Ma, Peter W. Arzberger, Wilfred W. Li	Customized Plug-in Modules in Metascheduler CSF4 for Life Sciences Applications.	New Gener. Comput.	2007	DBLP DOI BibTeX RDF	Metascheduling, Scheduler Plug-in, Co-Allocation, Life Sciences, MPICH-G2
23	Andrei Oliveira da Silva, Osmar Norberto de Souza	A framework for result handling in bioinformatics: an application to computer assisted drug design.	SAC	2005	DBLP DOI BibTeX RDF	computer assisted drug design, frameworks, bioinformatics, molecular docking, high-throughput computing
23	Michela Taufer, Michael F. Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III	Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics.	IPDPS	2004	DBLP DOI BibTeX RDF	Force field based methods, docking accuracy, desktop grid computing