BIGNASim
NAR Molecular Biology Database Collection entry number 1845
GelpÃÂ, Josep LluÃÂs; Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo; Battistini, Federica; Torres, Jordi; Goñi, Ramon; Orozco, Modesto
1Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and
Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.
2Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
3Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain.
4Department of Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain
5Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain.
2Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
3Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain.
4Department of Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain
5Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain.
Contact gelpi@ub.edu
Database Description
Atomistic Molecular Dynamics Simulation Trajectories and Analyses of Nucleic Acid Structures.
BIGNASim is a complete platform to hold and analyse nucleic acids simulation data, based on two noSQL database engines: Cassandra to hold trajectory data and MongoDB for analyses and metadata. Most common analyses (helical parameters, NMR observables, sitffness, hydrogen bonding and stacking energies and geometries) are pre-calculated for the trajectories available and shown using the interactive visualization offered by NAFlex interface. Additionaly, whole trajectories, fragments or meta-trajectories can be analysed or downloaded for further in-house processing.
BIGNASim is a complete platform to hold and analyse nucleic acids simulation data, based on two noSQL database engines: Cassandra to hold trajectory data and MongoDB for analyses and metadata. Most common analyses (helical parameters, NMR observables, sitffness, hydrogen bonding and stacking energies and geometries) are pre-calculated for the trajectories available and shown using the interactive visualization offered by NAFlex interface. Additionaly, whole trajectories, fragments or meta-trajectories can be analysed or downloaded for further in-house processing.
Acknowledgements
We are indebted to the members of the ABC consortium for many discussions, and the parmBSC1
contributors for the BIGNASim initial data set. We thank Dmitry Repchevsky for useful discussions
about BIGNASim ontology.
References
1. Ivani, I., Dans, P.D., Noy, A., Pérez, A., Faustino, I., Hospital A., Walther, J. et al. (2015)
Parmbsc1: a refined force field for DNA simulations, Nature Methods, Brief Communications, early
access. DOI: 10.1038/nmeth.3658.
2. Pasi, M., Maddocks, J.H., Beveridge, D., Bishop, T.C., Case, D.A., Cheatham, T. III, Dans, P.D., Jayaram, B., Lankas, F., Laughton, C. et al. (2014) muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res., 42, 12272- 12283.
3. Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D., Zakrzewska, K (2009) Conformational analysis of nucleic acids revisited: Curves. Nucleic Acids Res., 37, 5917-5929
4. Hospital, A., Faustino, I., Collepardo-Guevara, R., Gonzalez, C., Gelpi, J.L., Orozco, M. (2013) NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res., 41, W47-W55.
2. Pasi, M., Maddocks, J.H., Beveridge, D., Bishop, T.C., Case, D.A., Cheatham, T. III, Dans, P.D., Jayaram, B., Lankas, F., Laughton, C. et al. (2014) muABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res., 42, 12272- 12283.
3. Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D., Zakrzewska, K (2009) Conformational analysis of nucleic acids revisited: Curves. Nucleic Acids Res., 37, 5917-5929
4. Hospital, A., Faustino, I., Collepardo-Guevara, R., Gonzalez, C., Gelpi, J.L., Orozco, M. (2013) NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res., 41, W47-W55.
Category: Structure Databases
Subcategory: Nucleic acid structure
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