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MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
2012
Computer applications in the biosciences : CABIOS
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MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. ...
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). ...
ACKNOWLEDGEMENT We are indebted all the beta-testers of the platform. ...
doi:10.1093/bioinformatics/bts139
pmid:22437851
fatcat:hbp74nj5jfh63ebhqq3yy7ieea
BioExcel Webinar #3 - Atomistic Molecular Dynamics Setup with MDWeb
2016
Zenodo
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MDWeb [5] is a web server designed to ease this first contact with MD simulation. ...
A series of tools and databases offering an integrated approach to study macromolecular flexibility have been developed in IRB Barcelona. ...
• Molecular Dynamics: use limitations.
• MoDEL, MDMoby & MDWeb.
• • MDWeb Analysis: Basic Analysis & FlexServ.
• IRB Web Servers.
• MD & Flexibility: FlexServ, NAFlex. ...
doi:10.5281/zenodo.3775862
fatcat:efengya4wbghngwhwnm4xshbou
Bioexcel Deliverable 2.1 – State Of The Art And Gap Analysis
2016
Zenodo
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Based o [...] ...
For the interoperability issue, we found that the need for manual interaction needs to be reduced, for instance by incorporating workflow managers to integrate processes and input/output data. ...
-
-
Expert users interested in
quantum mechanics
simulations
MDWeb
IRB
Web
Portal
Web
No
-
Non-experts users
interested in Molecular
Dynamics simulations
MDMoby
IRB
Web
Services / ...
doi:10.5281/zenodo.263963
fatcat:o2v7ogjmnbauhn7txp2buz3pem
Molecular dynamics simulations: advances and applications
2015
Advances and Applications in Bioinformatics and Chemistry
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Biology, 3Barcelona Supercomputing Center, 4Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain Abstract: Molecular dynamics simulations have evolved into a mature ...
Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. ...
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics . 2012;28(9):1278–1279.
92.
Monod J, Changeux JP, Jacob F. ...
doaj:901fd7fe2a8145d880f02eb3e58dcf2d
fatcat:wis63q3cznchhcjxbe2qvrekcu
MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories
2010
Structure
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More than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means of state-of-the-art atomistic molecular dynamics simulations ...
The trajectories and analyses are stored in a large data warehouse, which can be queried for dynamic information on proteins, including interactions. ...
Sergi Girona and the MareNostrum support team for making this project possible. Helpful comments from Prof. F. J. Luque and many colleagues at IRB Barcelona and the BSC are gratefully acknowledged. ...
doi:10.1016/j.str.2010.07.013
pmid:21070939
fatcat:jyc64i63grap5hvenuwwjppvyu
IN SILICO SCREENING AND MOLECULAR DYNAMIC SIMULATION STUDIES OF POTENTIAL SMALL MOLECULE IMMUNOMODULATORS OF THE KIR2DS2 RECEPTOR
[article]
2020
bioRxiv
pre-print
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Analyses of molecular dynamic simulation were done using Galaxy and MDWEB webservers. ...
Keywords: KIR2DS2, NK Cells, ligands, Molecular Docking, Molecular Dynamics Simulation ...
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.Bioinformatics, 28(9):1278-1279.
. to estimate solubility and permeability in drug discovery and development settings ...
doi:10.1101/2020.05.10.087148
fatcat:g5fxn3yzkffltpnchhdrtw2hm4