The structures obtained from homology modeling methods are of intermediate resolution 1-3Ã… from true structure. Energy minimization methods allow us to refine the proteins and obtain native like structures. Previous work shows that some of these methods performed well on soluble proteins. So we extended this work on membrane proteins. Prediction of membrane protein structures is a particularly important, since they are important biological drug targets, and since their number is vanishingly small, as a result of the inherent difficulties in working with these molecules experimentally. Hence there is a pressing need for alternative computational protein structure prediction methods. This work tests the ability of common molecular mechanics potential functions (AMBER99/03) and a hybrid knowledge-based potential function (KB_0.1) to refine near-native structures of membrane proteins in vacuo. A web based utility for protein refinement has been developed and deployed based on the KB_0.1 potential to refine proteins.
","abstract_html":"<p>The structures obtained from homology modeling methods are of intermediate resolution 1-3Ã… from true structure. Energy minimization methods allow us to refine the proteins and obtain native like structures. Previous work shows that some of these methods performed well on soluble proteins. So we extended this work on membrane proteins. Prediction of membrane protein structures is a particularly important, since they are important biological drug targets, and since their number is vanishingly small, as a result of the inherent difficulties in working with these molecules experimentally. Hence there is a pressing need for alternative computational protein structure prediction methods. This work tests the ability of common molecular mechanics potential functions (AMBER99/03) and a hybrid knowledge-based potential function (KB_0.1) to refine near-native structures of membrane proteins in vacuo. A web based utility for protein refinement has been developed and deployed based on the KB_0.1 potential to refine proteins.</p>","abstract_has_math":false,"creators":["Pothakanoori, Kapil"],"institution":null,"degree_name":"M.S.","degree_level":"Thesis-Restricted","degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":["Summa, Christopher","Taylor, Christopher","Rick, Steven"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2010,"date_issued":"2010-12-17T08:00:00Z","date_published":"2010-12-17T08:00:00Z","updated_at":"2026-07-24T05:28:04Z","subjects":["Protein refinement Web server","membrane proteins","protein refinement","amber03/99","Knowledge based mechanics model"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://scholarworks.uno.edu/td/102","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Summa, Christopher","Taylor, Christopher","Rick, Steven"]},{"key":"dc:creator","label":"Author","values":["Pothakanoori, Kapil"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_discipline","label":"Discipline","values":["Computer Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis-Restricted"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Protein refinement Web server","membrane proteins","protein refinement","amber03/99","Knowledge based mechanics model"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://scholarworks.uno.edu/td/102"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The structures obtained from homology modeling methods are of intermediate resolution 1-3Ã… from true structure. Energy minimization methods allow us to refine the proteins and obtain native like structures. Previous work shows that some of these methods performed well on soluble proteins. So we extended this work on membrane proteins. Prediction of membrane protein structures is a particularly important, since they are important biological drug targets, and since their number is vanishingly small, as a result of the inherent difficulties in working with these molecules experimentally. Hence there is a pressing need for alternative computational protein structure prediction methods. This work tests the ability of common molecular mechanics potential functions (AMBER99/03) and a hybrid knowledge-based potential function (KB_0.1) to refine near-native structures of membrane proteins in vacuo. A web based utility for protein refinement has been developed and deployed based on the KB_0.1 potential to refine proteins.
"]},{"key":"dc:title","label":"Title","values":["A Web Service for Protein Refinement and Refinement of Membrane Proteins"]}]}],"canonical_facts":{"dc:contributor":["Summa, Christopher","Taylor, Christopher","Rick, Steven"],"dc:creator":["Pothakanoori, Kapil"],"dc:description.abstract":["The structures obtained from homology modeling methods are of intermediate resolution 1-3Ã… from true structure. Energy minimization methods allow us to refine the proteins and obtain native like structures. Previous work shows that some of these methods performed well on soluble proteins. So we extended this work on membrane proteins. Prediction of membrane protein structures is a particularly important, since they are important biological drug targets, and since their number is vanishingly small, as a result of the inherent difficulties in working with these molecules experimentally. Hence there is a pressing need for alternative computational protein structure prediction methods. This work tests the ability of common molecular mechanics potential functions (AMBER99/03) and a hybrid knowledge-based potential function (KB_0.1) to refine near-native structures of membrane proteins in vacuo. A web based utility for protein refinement has been developed and deployed based on the KB_0.1 potential to refine proteins.
"],"dc:identifier":["https://scholarworks.uno.edu/td/102"],"dc:subject":["Protein refinement Web server","membrane proteins","protein refinement","amber03/99","Knowledge based mechanics model"],"dc:title":["A Web Service for Protein Refinement and Refinement of Membrane Proteins"],"thesis:degree_discipline":["Computer Science"],"thesis:degree_level":["Thesis-Restricted"],"thesis:degree_name":["M.S."]},"updated_at":"2026-07-24T05:28:04Z"}