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HexServer: an FFT-based protein docking server powered by graphics processors

G. Macindoe, L. Mavridis, V. Venkatraman, M.-D. Devignes, D. W. Ritchie
2010 Nucleic Acids Research  
HexServer ( is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors.  ...  Using two graphics processors simultaneously, a typical 6D docking run takes $15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution  ...  These figures justify our claim that using GPUs to accelerate Hex docking calculations can be up to two orders of magnitude faster than conventional FFT-based docking approaches when using comparable search  ... 
doi:10.1093/nar/gkq311 pmid:20444869 pmcid:PMC2896144 fatcat:my4saqausndzncabdyc3bmkzsi

Ultra-fast FFT protein docking on graphics processors

David W. Ritchie, Vishwesh Venkatraman
2010 Computer applications in the biosciences : CABIOS  
Results: The Hex spherical polar Fourier protein docking algorithm has been implemented on Nvidia graphics processor units (GPUs).  ...  Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs.  ...  ACKNOWLEDGEMENTS We thank the Nvidia Professor Partner Programme for the gift of a graphics card. Funding: Agence Nationale de la Recherche, grant number ANR-08-CEXC-017-01.  ... 
doi:10.1093/bioinformatics/btq444 pmid:20685958 fatcat:3f6ig4iylbgxxp3ud7v76ydsc4

Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer

Sally R. Ellingson, Sivanesan Dakshanamurthy, Milton Brown, Jeremy C. Smith, Jerome Baudry
2013 Concurrency and Computation  
We describe a case study of using a task-parallel MPI (Message Passing Interface) version of Autodock4 [1], [2] to run a virtual high-throughput screen of one-million compounds on the Jaguar Cray XK6 Supercomputer  ...  We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis.  ...  Acknowledgments We thank Barbara Collignon for useful discussion and Kristina Thiagarajan for support.  ... 
doi:10.1002/cpe.3070 pmid:24729746 pmcid:PMC3979631 fatcat:3cwqn7mhxbhphfmtub6sexjsxe

GPU optimizations for a production molecular docking code

Raphael Landaverde, Martin C. Herbordt
2014 2014 IEEE High Performance Extreme Computing Conference (HPEC)  
graphics processors.  ...  Traditionally, graphics processors required graphics APIs such as OpenGL [Groa] .  ...  The car used infared sensors and SunSPOT processors to self navigate through a hallway and turn corners.  ... 
doi:10.1109/hpec.2014.7040981 pmid:26594667 pmcid:PMC4652941 dblp:conf/hpec/LandaverdeH14 fatcat:nne5ej4vfvbb7gywwy4qawxiuu

High performance transcription factor-DNA docking with GPU computing

Jiadong Wu, Bo Hong, Takako Takeda, Jun-tao Guo
2012 Proteome Science  
Methods: In an attempt to accelerate the sampling process and to improve the docking performance, we developed a graphics processing unit (GPU)-based protein-DNA docking algorithm.  ...  Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms.  ...  Acknowledgements This work was supported by the National Science Foundation #DBI-0844749 to JTG and #CNS-0845583 to BH.  ... 
doi:10.1186/1477-5956-10-s1-s17 pmid:22759575 pmcid:PMC3380734 fatcat:hoitcyrcwvgxlkvyjbl646ufz4

Molecular Docking for Ligand-Receptor Binding Process Based on Heterogeneous Computing

Jianhua Li, Guanlong Liu, Zhiyuan Zhen, Zihao Shen, Shiliang Li, Honglin Li, Basilio B. Fraguela
2022 Scientific Programming  
In this study, we propose a heterogeneous parallel scheme of molecular docking for the binding process of ligand to receptor to accelerate simulating.  ...  At the coarse-grain layer of parallelism, a docking task inside one lattice is assigned to one unique MPI process, and a grouped master-slave mode is used to allocate and schedule the tasks.  ...  Utilizing graphics processing unit (GPU) processors is the second way to accelerate docking applications [17] [18] [19] [20] [21] [22] .  ... 
doi:10.1155/2022/9197606 fatcat:wxdgjbicmve6lncosgpc6wqkwq

The impact of accelerator processors for high-throughput molecular modeling and simulation

G. Giupponi, M.J. Harvey, G. De Fabritiis
2008 Drug Discovery Today  
In conjunction with distributed and grid computing solutions, accelerated molecular simulations may finally be used to extend current in silico protocols by use of accurate thermodynamic calculations instead  ...  The recent introduction of cost-effective accelerator processors (APs), such as the IBM Cell processor and Nvidia's graphics processing units (GPUs), represents an important technological innovation which  ...  processors.  ... 
doi:10.1016/j.drudis.2008.08.001 pmid:18762274 fatcat:4lfl77txobdwxd6xnv32qbcwta

Recent Advances and Future Trend on the Emerging Role of GPUs as Platforms for Virtual Screening-Based Drug Discovery [chapter]

Horacio Prez-Snchez, Jos M., Jos M.
2012 Virtual Screening  
Driven by the demand of the game industry, Graphics Processing Units (GPUs) have completed a steady transition from mainframes to workstations to PC cards, where they emerge nowadays like a solid and compelling  ...  Both better scoring functions and novel docking strategies will contribute in this direction.  ...  ., 2006) approach for protein-ligand docking using GPUs.  ... 
doi:10.5772/35169 fatcat:3rzpjwks4zbxhosbegqy5q73ti

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski, Alexandre G. de Brevern
2016 PLoS ONE  
Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets  ...  Computational modeling of drug binding to proteins is an integral component of direct drug design.  ...  To address this problem, parallel computing is often used to accelerate docking simulations.  ... 
doi:10.1371/journal.pone.0158898 pmid:27420300 pmcid:PMC4946785 fatcat:z432fsbmmncvpje6h5rzwmliou

Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures

Takehiro Shimoda, Shuji Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama
2015 BMC Systems Biology  
docking calculation.  ...  Results: In the present study, we compared the effects of acceleration using graphics processing unit (GPU) and many integrated core (MIC) on the speed of fast Fourier transform (FFT)-based protein-protein  ...  Acknowledgements The authors would like to thank the TSUBAME supercomputer system at the Global Scientific Information and Computing Center (GSIC), Tokyo Institute of Technology.  ... 
doi:10.1186/1752-0509-9-s1-s6 pmid:25707855 pmcid:PMC4331681 fatcat:3j3k3ya54nenrnxsp5wejngske

GPU-accelerated molecular modeling coming of age

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, Klaus Schulten
2010 Journal of Molecular Graphics and Modelling  
that promises to become even more useful to molecular modeling.  ...  Modern GPUs have evolved into fully programmable, massively parallel co-processors that can now be exploited to accelerate many scientific computations, typically providing about one order of magnitude  ...  Ivan Ufimtsev would like to acknowledge an NVIDIA fellowship and National Science Foundation grant (CHE-06-26354).  ... 
doi:10.1016/j.jmgm.2010.06.010 pmid:20675161 pmcid:PMC2934899 fatcat:kced26vphjb7hpqhf5ygeazwfa

AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability

Pierre Darme, Manuel Dauchez, Arnaud Renard, Laurence Voutquenne-Nazabadioko, Dominique Aubert, Sandie Escotte-Binet, Jean-Hugues Renault, Isabelle Villena, Luiz-Angelo Steffenel, Stéphanie Baud
2021 International Journal of Molecular Sciences  
The reverse docking of a ligand on 87 proteins takes only 23 min on 1 GPU (Graphics Processing Unit), while version 1 required 300 cores to reach the same execution time.  ...  For instance, AMIDE version 2 allows acceleration of the docking up to 12.4 times for 100 runs of AutoDock compared to version 1, without significant changes in docking poses.  ...  However, the use of an on-board graphics processor is still possible.  ... 
doi:10.3390/ijms22147489 fatcat:463ity6pbjgt3gircjehrgaslq

Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs [chapter]

Ginés D. Guerrero, Horacio Pérez-Sánchez, Wolfgang Wenzel, José M. Cecilia, José M. García
2011 Advances in Intelligent and Soft Computing  
We empirically demonstrate that GPUs are well suited architecture for the acceleration of non-bonded interaction kernels, obtaining up to a 260 times sustained speedup compared to its sequential counterpart  ...  In this work we discuss the benefits of using massively parallel architectures for the optimization of Virtual Screening methods.  ...  This kernel is widely used and implemented in several VS methods, concretely the docking program FlexScreen [2] .  ... 
doi:10.1007/978-3-642-19914-1_9 dblp:conf/pacbb/GuerreroSWCG11 fatcat:5o4iio45nje3zhtqoe3wfhdygu

Hardware Accelerated Molecular Docking: A Survey [chapter]

Imre Pechan, Bela Feher
2012 Bioinformatics  
Acknowledgement We would like to thank evopro Informatics and Automation Ltd for supporting our work and providing access to the necessary hardware and software tools. References  ...  The protein is represented with 3D grids during docking making the protein-ligand energy calculation more effective.  ...  Calculating pairwise potentials Reference [38] focuses on the acceleration of calculating the pairwise potentials between the protein-ligand atoms.  ... 
doi:10.5772/48125 fatcat:lfksj4c3wfewpiyydhvjkazveu

Redesigning Vina@QNLM for Ultra-Large-Scale Molecular Docking and Screening on a Sunway Supercomputer

Hao Lu, Zhiqiang Wei, Cunji Wang, Jingjing Guo, Yuandong Zhou, Zhuoya Wang, Hao Liu
2021 Frontiers in Chemistry  
In some existing applications, we used Vina@QNLM to dock more than 10 million molecules to nine rigid proteins related to SARS-CoV-2 within 8.5 h on 10 million cores.  ...  Then, we readopted the core docking algorithm to incorporate the full advantage of the heterogeneous multicore processor architecture in intensive computing.  ...  For example, MolDock (Thomsen and Christensen, 2006) was used in the multithreading technology to accelerate the calculation process.  ... 
doi:10.3389/fchem.2021.750325 pmid:34778205 pmcid:PMC8581564 fatcat:a7yw6xc5qje4nd3dn36bbyoyua
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