These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
2. Managing Complex Workflows in Bioinformatics: An Interactive Toolkit With GPU Acceleration. Welivita A; Perera I; Meedeniya D; Wickramarachchi A; Mallawaarachchi V IEEE Trans Nanobioscience; 2018 Jul; 17(3):199-208. PubMed ID: 29994533 [TBL] [Abstract][Full Text] [Related]
3. Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics. Zheng M; Li X; Guo L J Mol Graph Model; 2013 Apr; 41():1-11. PubMed ID: 23454611 [TBL] [Abstract][Full Text] [Related]
4. Native structure-based modeling and simulation of biomolecular systems per mouse click. Lutz B; Sinner C; Bozic S; Kondov I; Schug A BMC Bioinformatics; 2014 Aug; 15(1):292. PubMed ID: 25176255 [TBL] [Abstract][Full Text] [Related]
5. BioWMS: a web-based Workflow Management System for bioinformatics. Bartocci E; Corradini F; Merelli E; Scortichini L BMC Bioinformatics; 2007 Mar; 8 Suppl 1(Suppl 1):S2. PubMed ID: 17430564 [TBL] [Abstract][Full Text] [Related]
6. Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations. Ieong PU; Sørensen J; Vemu PL; Wong CW; Demir Ö; Williams NP; Wang J; Crawl D; Swift RV; Malmstrom RD; Altintas I; Amaro RE Procedia Comput Sci; 2014; 29():1745-1755. PubMed ID: 29399238 [TBL] [Abstract][Full Text] [Related]
7. ST-analyzer: a web-based user interface for simulation trajectory analysis. Jeong JC; Jo S; Wu EL; Qi Y; Monje-Galvan V; Yeom MS; Gorenstein L; Chen F; Klauda JB; Im W J Comput Chem; 2014 May; 35(12):957-63. PubMed ID: 24638223 [TBL] [Abstract][Full Text] [Related]
8. AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability. Darme P; Dauchez M; Renard A; Voutquenne-Nazabadioko L; Aubert D; Escotte-Binet S; Renault JH; Villena I; Steffenel LA; Baud S Int J Mol Sci; 2021 Jul; 22(14):. PubMed ID: 34299110 [TBL] [Abstract][Full Text] [Related]
9. MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. Gecht M; Siggel M; Linke M; Hummer G; Köfinger J J Chem Phys; 2020 Oct; 153(14):144105. PubMed ID: 33086826 [TBL] [Abstract][Full Text] [Related]
10. MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics. Brueckner AC; Shields B; Kirubakaran P; Suponya A; Panda M; Posy SL; Johnson S; Lakkaraju SK J Comput Aided Mol Des; 2024 Jul; 38(1):24. PubMed ID: 39014286 [TBL] [Abstract][Full Text] [Related]
11. A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. Yang PC; Purawat S; Ieong PU; Jeng MT; DeMarco KR; Vorobyov I; McCulloch AD; Altintas I; Amaro RE; Clancy CE PLoS Comput Biol; 2019 Mar; 15(3):e1006856. PubMed ID: 30849072 [TBL] [Abstract][Full Text] [Related]
12. JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing. Brown DK; Penkler DL; Musyoka TM; Bishop ÖT PLoS One; 2015; 10(8):e0134273. PubMed ID: 26280450 [TBL] [Abstract][Full Text] [Related]
13. ClickMD: an intuitive web-oriented molecular dynamics platform. Cristiani A; Brisotto N; Cedrati FC; Floris M; Scapozza L; Moro S Future Med Chem; 2011 Jun; 3(8):923-31. PubMed ID: 21707396 [TBL] [Abstract][Full Text] [Related]
14. A web services choreography scenario for interoperating bioinformatics applications. de Knikker R; Guo Y; Li JL; Kwan AK; Yip KY; Cheung DW; Cheung KH BMC Bioinformatics; 2004 Mar; 5():25. PubMed ID: 15113410 [TBL] [Abstract][Full Text] [Related]
15. EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins. Suplatov D; Sharapova Y; Švedas V J Bioinform Comput Biol; 2020 Dec; 18(6):2040011. PubMed ID: 32833550 [TBL] [Abstract][Full Text] [Related]
16. Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study. Singh H; Raja A; Prakash A; Medhi B J Chem Inf Model; 2023 May; 63(9):2603-2608. PubMed ID: 37079775 [TBL] [Abstract][Full Text] [Related]
17. Sharing Data from Molecular Simulations. Abraham M; Apostolov R; Barnoud J; Bauer P; Blau C; Bonvin AMJJ; Chavent M; Chodera J; Čondić-Jurkić K; Delemotte L; Grubmüller H; Howard RJ; Jordan EJ; Lindahl E; Ollila OHS; Selent J; Smith DGA; Stansfeld PJ; Tiemann JKS; Trellet M; Woods C; Zhmurov A J Chem Inf Model; 2019 Oct; 59(10):4093-4099. PubMed ID: 31525920 [TBL] [Abstract][Full Text] [Related]
18. From the desktop to the grid: scalable bioinformatics via workflow conversion. de la Garza L; Veit J; Szolek A; Röttig M; Aiche S; Gesing S; Reinert K; Kohlbacher O BMC Bioinformatics; 2016 Mar; 17():127. PubMed ID: 26968893 [TBL] [Abstract][Full Text] [Related]
19. BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. Bayarri G; Andrio P; Hospital A; Orozco M; Gelpí JL Nucleic Acids Res; 2022 Jul; 50(W1):W99-W107. PubMed ID: 35639735 [TBL] [Abstract][Full Text] [Related]
20. Biowep: a workflow enactment portal for bioinformatics applications. Romano P; Bartocci E; Bertolini G; De Paoli F; Marra D; Mauri G; Merelli E; Milanesi L BMC Bioinformatics; 2007 Mar; 8 Suppl 1(Suppl 1):S19. PubMed ID: 17430563 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]