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MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations

Adam Hospital, Pau Andrio, Carles Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluís Gelpí
2012 Computer applications in the biosciences : CABIOS  
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

Adam Hospital
2016 Zenodo  
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

Adam Hospital, Anna Montras, Stian Soiland-Reyes, Alexandre Bonvin, Adrien Melquiond, Josep Lluís Gelpí, Daniele Lezzi, Steven Newhouse, Jose A. Dianes, Mark Abraham, Rossen Apostolov, Emiliano Ippoliti (+2 others)
2016 Zenodo  
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

Hospital A, Goñi JR, Orozco M, Gelpí JL
2015 Advances and Applications in Bioinformatics and Chemistry  
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

Tim Meyer, Marco D'Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluis Gelpí, Modesto Orozco
2010 Structure  
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]

Adekunle Babajide Rowaiye, Olujide Oludayo Olubiyi, Doofan Bur, Ikemefuna Chijioke Uzochukwu, Alex Akpa, Charles Okechukwu Esimone
2020 bioRxiv   pre-print
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