Academic Journal
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
| Τίτλος: | BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations |
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| Συγγραφείς: | Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluís Gelpí |
| Συνεισφορές: | Barcelona Supercomputing Center |
| Πηγή: | Nucleic Acids Res Articles publicats en revistes (Bioquímica i Biomedicina Molecular) Dipòsit Digital de la UB instname UPCommons. Portal del coneixement obert de la UPC Universitat Politècnica de Catalunya (UPC) Universidad de Barcelona |
| Στοιχεία εκδότη: | Oxford University Press (OUP), 2022. |
| Έτος έκδοσης: | 2022 |
| Θεματικοί όροι: | Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], Internet, Molecular biology, BioExcel Building Blocks, Proteins, Molecular dynamics, Molecular Dynamics Simulation, Ligands, Graphical user interfaces (Computer systems), Workflow, Molecular Docking Simulation, User-Computer Interface, Cicle de treball, Simulació per ordinador, Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Web Server Issue, Interfícies gràfiques d'usuari (Informàtica), Biomolecular simulations, Software, Biologia molecular |
| Περιγραφή: | We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users’ own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users’ projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs. |
| Τύπος εγγράφου: | Article Other literature type |
| Περιγραφή αρχείου: | application/pdf |
| Γλώσσα: | English |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkac380 |
| DOI: | 10.13039/100010661 |
| Σύνδεσμος πρόσβασης: | https://pubmed.ncbi.nlm.nih.gov/35639735 https://hdl.handle.net/2445/189875 http://hdl.handle.net/2445/189875 |
| Rights: | CC BY NC |
| Αριθμός Καταχώρησης: | edsair.doi.dedup.....f7dda3121e5b31c282eaebafeb0328c9 |
| Βάση Δεδομένων: | OpenAIRE |
| ISSN: | 13624962 03051048 |
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| DOI: | 10.1093/nar/gkac380 |