{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T00:03:20Z","timestamp":1744157000360},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,1]]},"abstract":"Abstract<\/jats:title>\n Summary: MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http:\/\/mmb.pcb.ub.es\/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb).<\/jats:p>\n Availability: \u00a0http:\/\/mmb.irbbarcelona.org\/MDWeb; additional information and methodology details can be found at the web site (http:\/\/mmb.irbbarcelona.org\/MDWeb\/help.php)<\/jats:p>\n Contact: \u00a0gelpi@ub.edu; modesto.orozco@irbbarcelona.org<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts139","type":"journal-article","created":{"date-parts":[[2012,3,23]],"date-time":"2012-03-23T02:26:18Z","timestamp":1332469578000},"page":"1278-1279","source":"Crossref","is-referenced-by-count":150,"title":["MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations"],"prefix":"10.1093","volume":"28","author":[{"given":"Adam","family":"Hospital","sequence":"first","affiliation":[{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"},{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"}]},{"given":"Pau","family":"Andrio","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"},{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"}]},{"given":"Carles","family":"Fenollosa","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"},{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"}]},{"given":"Damjan","family":"Cicin-Sain","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"},{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"}]},{"given":"Modesto","family":"Orozco","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"},{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"},{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 643, Barcelona 08028, Spain"}]},{"given":"Josep Llu\u00eds","family":"Gelp\u00ed","sequence":"additional","affiliation":[{"name":"1 Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028, and Barcelona Supercomputing Center, Jordi Girona 31, Barcelona 08034, 2Structural Bioinformatics Node, National Institute of Bioinformatics, Josep Samitier 1-5, Barcelona 08028, 3Computatinal Bioinformatics Node, National Institute of Bioinformatics, Jordi Girona 31, Barcelona 08034 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. 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