{"id":{"repo_id":"umn","oai_identifier":"oai:conservancy.umn.edu:11299/160352"},"canonical_url":"https://search.dev.ndltd.org/etd/umn/oai:conservancy.umn.edu:11299/160352","repository":{"repo_id":"umn","name":"University of Minnesota","base_url":"https://conservancy.umn.edu/server/oai/request"},"display":{"title":"Consistent approach for calculating protein pKa's using Poisson-Boltzmann Model","abstract":"Accurate prediction of protein pKa`s is important to understand protein electrostatics and functions. Improving the accuracy of pKa prediction using the Poisson-Boltzmann electrostatic model remains an active area of research. The major challenge is to determine the appropriate dielectric constant that best describes the heterogeneous protein environment. The common use of a single large dielectric constant often fails to reproduce large experimental pKa shifts of biological important residues. In this study, I implemented a two steps approach, as described in earlier PDLD/S model, that uses a single low dielectric constant for calculating the intrinsic protein pKa`s when all other ionizable group are neutralized and a single large dielectric constant for evaluating the pKa`s shifts as a result of charge-charge coupling between ionizable groups. This approach is less sensitive to the dielectric constants used and can reliably reproduce the commonly observed protein pKa`s and others with abnormal large pKa shifts.","abstract_html":"Accurate prediction of protein pKa`s is important to understand protein electrostatics and functions. Improving the accuracy of pKa prediction using the Poisson-Boltzmann electrostatic model remains an active area of research. The major challenge is to determine the appropriate dielectric constant that best describes the heterogeneous protein environment. The common use of a single large dielectric constant often fails to reproduce large experimental pKa shifts of biological important residues. In this study, I implemented a two steps approach, as described in earlier PDLD/S model, that uses a single low dielectric constant for calculating the intrinsic protein pKa`s when all other ionizable group are neutralized and a single large dielectric constant for evaluating the pKa`s shifts as a result of charge-charge coupling between ionizable groups. This approach is less sensitive to the dielectric constants used and can reliably reproduce the commonly observed protein pKa`s and others with abnormal large pKa shifts.","abstract_has_math":false,"creators":["Yoon, Han Wool"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2013,"date_issued":"2013-06","date_published":"2013-06","updated_at":"2026-07-24T05:20:01Z","subjects":["Dielectric constant","PDLD/S","pKa calculation in protein","Poisson Boltzmann Model","protein pKa"],"languages":["en_US"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://purl.umn.edu/160352","outbound_label":"Repository record","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Yoon, Han Wool"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2013-11-15T21:42:57Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2013-11-15T21:42:57Z"]},{"key":"dc:date.issued","label":"Date","values":["2013-06"]},{"key":"dc:type","label":"Dc Type","values":["Thesis or Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Dielectric constant","PDLD/S","pKa calculation in protein","Poisson Boltzmann Model","protein pKa"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_US"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://purl.umn.edu/160352"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["University of Minnesota M.S. thesis. June 2013. Major: Biomedical Informatics and Computational Biology. Advisor: Yuk Sham. 1 computer file (PDF); v, 55 pages, appendix A."]},{"key":"dc:description.abstract","label":"Abstract","values":["Accurate prediction of protein pKa`s is important to understand protein electrostatics and functions. Improving the accuracy of pKa prediction using the Poisson-Boltzmann electrostatic model remains an active area of research. The major challenge is to determine the appropriate dielectric constant that best describes the heterogeneous protein environment. The common use of a single large dielectric constant often fails to reproduce large experimental pKa shifts of biological important residues. In this study, I implemented a two steps approach, as described in earlier PDLD/S model, that uses a single low dielectric constant for calculating the intrinsic protein pKa`s when all other ionizable group are neutralized and a single large dielectric constant for evaluating the pKa`s shifts as a result of charge-charge coupling between ionizable groups. This approach is less sensitive to the dielectric constants used and can reliably reproduce the commonly observed protein pKa`s and others with abnormal large pKa shifts."]},{"key":"dc:title","label":"Title","values":["Consistent approach for calculating protein pKa's using Poisson-Boltzmann Model"]}]}],"canonical_facts":{"dc:creator":["Yoon, Han Wool"],"dc:date.accessioned":["2013-11-15T21:42:57Z"],"dc:date.available":["2013-11-15T21:42:57Z"],"dc:date.issued":["2013-06"],"dc:description":["University of Minnesota M.S. thesis. June 2013. Major: Biomedical Informatics and Computational Biology. Advisor: Yuk Sham. 1 computer file (PDF); v, 55 pages, appendix A."],"dc:description.abstract":["Accurate prediction of protein pKa`s is important to understand protein electrostatics and functions. Improving the accuracy of pKa prediction using the Poisson-Boltzmann electrostatic model remains an active area of research. The major challenge is to determine the appropriate dielectric constant that best describes the heterogeneous protein environment. The common use of a single large dielectric constant often fails to reproduce large experimental pKa shifts of biological important residues. In this study, I implemented a two steps approach, as described in earlier PDLD/S model, that uses a single low dielectric constant for calculating the intrinsic protein pKa`s when all other ionizable group are neutralized and a single large dielectric constant for evaluating the pKa`s shifts as a result of charge-charge coupling between ionizable groups. This approach is less sensitive to the dielectric constants used and can reliably reproduce the commonly observed protein pKa`s and others with abnormal large pKa shifts."],"dc:identifier.uri":["http://purl.umn.edu/160352"],"dc:language.iso":["en_US"],"dc:subject":["Dielectric constant","PDLD/S","pKa calculation in protein","Poisson Boltzmann Model","protein pKa"],"dc:title":["Consistent approach for calculating protein pKa's using Poisson-Boltzmann Model"],"dc:type":["Thesis or Dissertation"]},"updated_at":"2026-07-24T05:20:01Z"}