{"data":{"id":"10.6084/m9.figshare.799704.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.799704.v1","prefix":"10.6084","suffix":"m9.figshare.799704.v1","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Cooper, Christopher D.","nameType":"Personal","givenName":"Christopher D.","familyName":"Cooper","affiliation":[],"nameIdentifiers":[]},{"name":"Jaydeep Bardhan","affiliation":[],"nameIdentifiers":[]},{"name":"Barba, Lorena A.","nameType":"Personal","givenName":"Lorena A.","familyName":"Barba","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Binding energy of peptide-RNA complex with PyGBe and APBS"}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"subject":"Molecular Physics"},{"subject":"Computational Biology"},{"subject":"Computational Physics"},{"subject":"Mechanical Engineering"},{"subject":"FOS: Mechanical engineering","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Mechanical engineering","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Biophysics"}],"contributors":[],"dates":[{"date":"2013-09-15","dateType":"Created"},{"date":"2016-01-18","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsIdenticalTo","relatedIdentifier":"10.6084/m9.figshare.799704","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["15812294 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"This file bundle includes data, figures and plotting scripts of solvation energy and binding energy calculations for peptide-RNA complex using PyGBe and APBS. Errors were calculated with respect to the corresponding extrapolated values (obtained from Richardson extrapolation). This result is part of the paper: —\"A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers\", Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba. \u003cem\u003eComput. Phys. Comm.,\u003c/em\u003e \u003cstrong\u003e185\u003c/strong\u003e(3):720–729 (March 2014). 10.1016/j.cpc.2013.10.028 // Preprint arXiv:1309.4018 PyGBe solves biomolecular electrostatics problems using an implicit-solvent model (Poisson-Boltzmann) and it uses GPU hardware for fast execution. It is written in Python, PyCUDA and CUDA. More information about the PyGBe code in: \u003cem\u003e—Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods\u003c/em\u003e. Christopher Cooper, Lorena A. Barba. figshare.\u003cbr\u003ehttp://dx.doi.org/10.6084/m9.figshare.154331 \u003cstrong\u003eAcknowledgement:\u003c/strong\u003e\u003cbr\u003eThis research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program, N00014-11-1-0356. LAB also acknowledges support from NSF CAREER award OCI-1149784.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://figshare.com/articles/dataset/Binding_energy_of_peptide_RNA_complex_with_PyGBe_and_APBS/799704/1","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":3,"viewsOverTime":[{"yearMonth":"2025-06","total":1},{"yearMonth":"2025-07","total":1},{"yearMonth":"2026-05","total":1}],"downloadCount":0,"downloadsOverTime":[{"yearMonth":"2025-06","total":0},{"yearMonth":"2025-07","total":0},{"yearMonth":"2026-05","total":0}],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"par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