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SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches [article]

G.V. HarshaRani, Sahil Moza, Naren Ramakrishnan, Upinder S Bhalla
2020 bioRxiv   pre-print
The Searchable Web Interface for Topologies of CHEmical Switches (SWITCHES, https://switches.ncbs.res.in) provides a bistability and parameter analysis of over 7 million models from this systematic survey  ...  This database will be useful for theoreticians interested in analyzing stability in chemical systems and also experimentalists for creating robust synthetic biological switches.  ...  Interface and functional organisation of the SWITCHES database. The web interface supports searches by model topology, traversal through related models, and searches based on model solutions.  ... 
doi:10.1101/2020.08.04.232371 fatcat:75o4nvlwzjd25a43ewzbzlofiu

Web-based Metaprogrammable Frontend for Molecular Dynamics Simulations
english

Gergely Varga, Sara Toth, Christopher R. Iacovella, János Sallai, Péter Völgyesi, Ákos Lédeczi, Gabor Karsai, Peter T. Cummings
2013 Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications  
The web-based environment also supports setting up a suite of simulation jobs, for example, to carry out automated parameter optimization, via a visual programming environment.  ...  Molecular dynamics simulators are indispensable tools in the arsenal of chemical engineers and material scientists.  ...  Nevertheless, it provides a web-based interface for a variety of simulation softwares. However, the interface is somewhat unusual.  ... 
doi:10.5220/0004486401710178 dblp:conf/simultech/VargaTISVLKC13 fatcat:vwuqs3hhezhcrbavkrmwtgopom

On Different Aspects of Network Analysis in Systems Biology [chapter]

Amphun Chaiboonchoe, Wiktor Jurkowski, Johann Pellet, Enrico Glaab, Alexey Kolodkin, Antonio Raussel, Antony Le Béchec, Stéphane Ballereau, Laurene Meyniel, Isaac Crespo, Hassan Ahmed, Vitaly Volpert (+6 others)
2013 Systems Biology  
This chapter describes several types of biological networks, how combination of different analytic approaches can be used to study diseases, and provides a list of selected tools for network visualization  ...  Cellular processes depend on the structure and dynamics of gene regulatory networks and can be studied by employing a network representation of molecular interactions.  ...  We would like to acknowledge the support of the Luxembourg Centre for Systems Biomedicine and the University of Luxembourg (LH and RB), the NIH General Medical Sciences Center for Systems Biology GM076547  ... 
doi:10.1007/978-94-007-6803-1_6 fatcat:p2tlc43sazazlav3l3stp5qzk4

MolMeDB: Molecules on Membranes Database [article]

Jakub Juracka, Martin Srejber, Michaela Melikova, Vaclav Bazgier, Karel Berka
2018 bioRxiv   pre-print
The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method, or dataset and we offer the collected data openly for further reuse and we are open to further additions  ...  MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.  ...  Results and Discussion User Interface and Database Usage To provide a user-friendly interface for the molecule-membrane interaction data, we developed a web version of MolMeDB database, freely accessible  ... 
doi:10.1101/472167 fatcat:ai4witz5gfc2xckqoalpolunqe

MolMeDB: Molecules on Membranes Database

2019 Database: The Journal of Biological Databases and Curation  
The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method or dataset and we offer the collected data openly for further reuse and we are open to further additions  ...  MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/baz078 pmid:31250015 pmcid:PMC6597476 fatcat:rtropmkborghzhh73nwlrixccy

SwissDock, a protein-small molecule docking web service based on EADock DSS

A. Grosdidier, V. Zoete, O. Michielin
2011 Nucleic Acids Research  
For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP.  ...  This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins.  ...  ACKNOWLEDGEMENTS We thank the VITAL-IT project of the Swiss Institute of Bioinformatics (Lausanne, Switzerland) for providing part of the computational resources.  ... 
doi:10.1093/nar/gkr366 pmid:21624888 pmcid:PMC3125772 fatcat:2reyktuxqnhxzluvh2lukw6roi

SynBioSS-Aided Design of Synthetic Biological Constructs [chapter]

Yiannis N. Kaznessis
2011 Methods in Enzymology  
known synthetic biological systems, such as bistable switches, AND gates, and oscillators.  ...  SynBioSS-based modeling of biomolecular ensembles that interact away from the thermodynamic limit and not necessarily at steady state affords for a theoretical framework that is generally applicable to  ...  In addition, the author thanks Jon Tomshine, Ben Swiniarski, and Kostas Biliouris for help with the illustrations.  ... 
doi:10.1016/b978-0-12-385120-8.00006-1 pmid:21601676 pmcid:PMC4820535 fatcat:3vlyw5nby5barajfamogkgmt7i

What is the best or most relevant global minimum for nanoclusters? Predicting, comparing and recycling cluster structures with WASP@N

Scott M. Woodley, Tomas Lazauskas, Malcolm Illingworth, Adam C. Carter, Alexey A. Sokol
2018 Faraday discussions  
Our WASP@N project is an open-access database of cluster structures with a web-assisted interface and toolkit for structure prediction.  ...  Acknowledgements The creation of the Hive, WASP interface, and Bee soware are all part of the WASP@N ve-year project that is supported by EPSRC (grant numbers EP/ K038958, K038559).  ...  We are grateful for valuable discussions and help from our colleagues who are also part of this project, namely: Jörg Sassmannshausen Notes and references  ... 
doi:10.1039/c8fd00060c pmid:30067264 fatcat:7rna6a5hdbdipb3cweku3yzagm

Search, access, and explore life science nanopublications on the Web

Fabio Giachelle, Dennis Dosso, Gianmaria Silvello
2021 PeerJ Computer Science  
For the time being, NanoWeb focuses on the life science domain where the vastest amount of nanopublications are available.  ...  There are millions of nanopublications currently available on the Web, especially in the life science domain.  ...  ACKNOWLEDGEMENTS The authors wish to thank Erika Fabris for the work on the citation of nanopublications and the development of some APIs used in this work.  ... 
doi:10.7717/peerj-cs.335 pmid:33816986 pmcid:PMC7959622 fatcat:cxmldprn4fcezbiryjdsrwskfy

COEL: A Web-based Chemistry Simulation Framework [article]

Peter Banda, Drew Blount, Christof Teuscher
2014 arXiv   pre-print
COEL is the first web-based framework of its kind.  ...  The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems.  ...  We acknowledge Avi Debnath for his work on DNAstrand visualization, and GridGain for an academic license to use the GridGain HPC technology.  ... 
arXiv:1407.4027v1 fatcat:hsf65clgv5ekbpvq66uoqeclai

Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks [chapter]

Baltazar D. Aguda, Georghe Craciun, Rengul Cetin-Atalay
2005 Reviews in computational chemistry  
of an additional web-browser.  ...  E-Cell provides several graphical interfaces for user definable models of certain cellular states.  ... 
doi:10.1002/0471720895.ch6 fatcat:iaodscfur5e3pjy2z2oejtufyy

JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology

Mary Ann Blätke, Anna Dittrich, Christian Rohr, Monika Heiner, Fred Schaper, Wolfgang Marwan
2013 Molecular Biosystems  
We describe a molecule-oriented modelling approach based on a collection of Petri net models organized in the form of modules into a prototype database accessible through a web interface.  ...  Each module contains metadata for documentation purposes and can be extended to a wiki-like minireview. The database can manage multiple versions of each module.  ...  Acknowledgemnts We thank Professor David Gilbert for critical reading of the manuscript and for suggesting module based automatic biomodel engineering and its application to  ... 
doi:10.1039/c3mb25593j pmid:23443149 fatcat:6c2ttcuimffd3d5aezzpapg4ce

A comprehensive data acquisition and management system for an ecosystem-scale peatland warming and elevated CO2 experiment

M. B. Krassovski, J. S. Riggs, L. A. Hook, W. R. Nettles, P. J. Hanson, T. A. Boden
2015 Geoscientific Instrumentation Methods and Data Systems Discussions  
SPRUCE provides a platform for testing mechanisms controlling the vulnerability of organisms, biogeochemical processes, and ecosystems to climatic change (e.g., thresholds for organism decline or mortality  ...  Data collection system – set of hardware and software to deliver data to a central depository for storage and further processing.<br> 3.  ...  UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725.  ... 
doi:10.5194/gid-5-177-2015 fatcat:wfq4akyttfa4zaysy5e32qsepe

A comprehensive data acquisition and management system for an ecosystem-scale peatland warming and elevated CO2 experiment

M. B. Krassovski, J. S. Riggs, L. A. Hook, W. R. Nettles, P. J. Hanson, T. A. Boden
2015 Geoscientific Instrumentation, Methods and Data Systems  
SPRUCE provides a platform for testing mechanisms controlling the vulnerability of organisms, biogeochemical processes, and ecosystems to climatic change (e.g., thresholds for organism decline or mortality  ...  <br> This publication presents our approach to meeting the challenges of designing and constructing an efficient data system for managing high volume sources of in situ observations in a remote, harsh  ...  UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725.  ... 
doi:10.5194/gi-4-203-2015 fatcat:vddb7s2mvjg4dlqc7ofhp3ch4q

Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction

Anna W. Baker, Kenneth A. Satyshur, Neydis Moreno Morales, Katrina T. Forest, A. M. Stock
2016 Journal of Bacteriology  
Monomerization via deletion of the C-terminal dimerization motif had an inhibitory effect on net response regulator phosphorylation, underlining the importance of these unusual dimers for signal transduction  ...  To begin to address this knowledge gap, we solved the crystal structures of two single-domain response regulators encoded by a region immediately downstream of that encoding BphPs.  ...  ACKNOWLEDGMENTS We thank Kittikhun Wangkonant for data collection assistance, Thierry Heulin for supplying R. tataouinensis strain TTB310, and Michael Thomas for the use of equipment and facilities.  ... 
doi:10.1128/jb.00872-15 pmid:26833410 pmcid:PMC4859592 fatcat:khxdc6gblzfcjamrxejgdspvw4
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