{"data":{"id":"10.6084/m9.figshare.799703.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.799703.v1","prefix":"10.6084","suffix":"m9.figshare.799703.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 trypsin-BPTI 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.799703","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["37078022 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 trypsin-BPTI 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_trypsin_BPTI_complex_with_PyGBe_and_APBS/799703/1","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":13,"viewsOverTime":[{"yearMonth":"2025-03","total":3},{"yearMonth":"2025-03","total":3},{"yearMonth":"2025-04","total":2},{"yearMonth":"2025-04","total":2},{"yearMonth":"2026-01","total":1},{"yearMonth":"2026-05","total":1},{"yearMonth":"2026-06","total":1}],"downloadCount":0,"downloadsOverTime":[{"yearMonth":"2025-03","t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