Publications

Robert T. McGibbon, Kyle A. Beauchamp, Matthew P. Harrigan, Christoph Klein, Jason M. Swails, Carlos X. Hernández, Christian R. Schwantes, Lee-Ping Wang, Thomas J. Lane, and Vijay S. Pande. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal, (109)8:1528 -- 1532, 2015. [PUMA: forschungsdaten molecularSimulation software]

Martin Thomas Horsch, Christoph Niethammer, Gianluca Boccardo, Paola Carbone, Silvia Chiacchiera, Mara Chiricotto, Joshua D. Elliott, Vladimir Lobaskin, Philipp Neumann, Peter Schiffels, Michael A. Seaton, Ilian T. Todorov, Jadran Vrabec, and Welchy Leite Cavalcanti. Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering. Journal of Chemical & Engineering Data, (65)3:1313--1329, American Chemical Society (ACS), December 2019. [PUMA: forschungsdaten hpc-computing metadata molecularSimulation ontologie] URL

Anand Kumar, Vladimir Grupcev, Meryem Berrada, Joseph C. Fogarty, Yi-Cheng Tu, Xingquan Zhu, Sagar A. Pandit, and Yuni Xia. DCMS: A data analytics and management system for molecular simulation. Journal of Big Data, (2)1:9, Nov 26, 2014. [PUMA: imported molecularSimulation obib] URL

G. Finocchiaro, T. Wang, R. Hoffmann, A. Gonzalez, and R. Wade. DSMM: a database of simulated molecular motions. Nucleic Acids Res, (31)2003. [PUMA: imported molecularSimulation] URL

M. H. Ng, S. Johnston, B. Wu, S. E. Murdock, K. Tai, H. Fangohr, S. J. Cox, J. W. Essex, M. S. P. Sansom, and P. Jeffreys. BioSimGrid: grid-enabled biomolecular simulation data storage and analysis. Future Generation Comput Systs, (22)2006. [PUMA: imported molecularSimulation] URL

M. van der Kamp, R. Schaeffer, A. Jonsson, A. Scouras, A. Simms, R. Toofanny, N. Benson, P. Anderson, E. Merkley, S. Rysavy, D. Bromley, D. Beck, and V. Daggett. Dynameomics: a comprehensive database of protein dynamics. Structure, (18)2010. [PUMA: imported molecularSimulation] URL

M. Feig, M. Abdullah, L. Johnsson, and B. M. Pettitt. Large scale distributed data repository: design of a molecular dynamics trajectory database. Future Generation Comput Syst, (16)1999. [PUMA: imported molecularSimulation] URL

W. Humphrey, A. Dalke, and K. Shulten. VMD: visual molecular dynamics. J Mol Graph, (14)1996. [PUMA: imported molecularSimulation] URL

A. Chapman, H. V. Jagadish, and P. Ramanan. Efficient provenance storage. ACM, Vancouver, BC, Canada, 2008. [PUMA: imported molecularSimulation]

N. Michaud-Agrawal, E. Denning, T. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J Comput Chem, (32)2011. [PUMA: imported molecularSimulation] URL