{"id":{"repo_id":"soton","oai_identifier":"oai:eprints.soton.ac.uk:173851"},"canonical_url":"https://search.dev.ndltd.org/etd/soton/oai:eprints.soton.ac.uk:173851","repository":{"repo_id":"soton","name":"University of Southampton","base_url":"https://eprints.soton.ac.uk/cgi/oai2"},"display":{"title":"Modelling protein backbone loops using the Monte Carlo method","abstract":"Novel methods that perform local moves such as the gaussian bias or Con-<br/>certed Rotation with Angles, increase the exploration of the conformational<br/>phase space. These methods have been applied successfully to small systems,<br/>and have proved to be more efficient than the classical Monte Carlo method.<br/><br/>The main aim of my work was to study and include backbone moves<br/>for proteins, such as the Concerted Rotation with Angle (CRA) and the<br/>gaussian bias in the ProtoMS package. The CRA was then applied to several<br/>systems of biological interest to compute relative binding free energies and<br/>conformational changes to obtain insights into the binding mode and system<br/>flexibility.<br/><br/>The CRA algorithm has been used to sample biological systems such<br/>as lysozyme L99A mutant, Bcr-Abl kinases and PDE5 phosphodiesterase<br/>and led to increased sampling of the backbone and more precise free energy<br/>results.","abstract_html":"Novel methods that perform local moves such as the gaussian bias or Con-&lt;br/&gt;certed Rotation with Angles, increase the exploration of the conformational&lt;br/&gt;phase space. These methods have been applied successfully to small systems,&lt;br/&gt;and have proved to be more efficient than the classical Monte Carlo method.&lt;br/&gt;&lt;br/&gt;The main aim of my work was to study and include backbone moves&lt;br/&gt;for proteins, such as the Concerted Rotation with Angle (CRA) and the&lt;br/&gt;gaussian bias in the ProtoMS package. The CRA was then applied to several&lt;br/&gt;systems of biological interest to compute relative binding free energies and&lt;br/&gt;conformational changes to obtain insights into the binding mode and system&lt;br/&gt;flexibility.&lt;br/&gt;&lt;br/&gt;The CRA algorithm has been used to sample biological systems such&lt;br/&gt;as lysozyme L99A mutant, Bcr-Abl kinases and PDE5 phosphodiesterase&lt;br/&gt;and led to increased sampling of the backbone and more precise free energy&lt;br/&gt;results.","abstract_has_math":false,"creators":["Fernandez-Carmona, Juan"],"institution":"University of Southampton","degree_name":"Ph.D.","degree_level":"doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Essex, Jonathan W."],"committee_chairs":[],"committee_members":[],"year":2009,"date_issued":"2009-04","date_published":"2009-04","updated_at":"2026-07-24T04:36:21Z","subjects":[],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":null,"outbound_label":null,"outbound_source":null},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Essex, Jonathan W."]},{"key":"dc:creator","label":"Author","values":["Fernandez-Carmona, Juan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2009-04-03"]},{"key":"dc:date.issued","label":"Date","values":["2009-04"]},{"key":"dc:publisher.department","label":"Dc Publisher Department","values":["Chemistry (pre 2011 reorg)","School of Chemistry"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Southampton"]},{"key":"dc:relation.isreferencedby","label":"Dc Relation Isreferencedby","values":["https://eprints.soton.ac.uk/173851/"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Ph.D."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://eprints.soton.ac.uk/173851/1/FERNANDEZ_CARMONA_Juan.pdf"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Novel methods that perform local moves such as the gaussian bias or Con-<br/>certed Rotation with Angles, increase the exploration of the conformational<br/>phase space. These methods have been applied successfully to small systems,<br/>and have proved to be more efficient than the classical Monte Carlo method.<br/><br/>The main aim of my work was to study and include backbone moves<br/>for proteins, such as the Concerted Rotation with Angle (CRA) and the<br/>gaussian bias in the ProtoMS package. The CRA was then applied to several<br/>systems of biological interest to compute relative binding free energies and<br/>conformational changes to obtain insights into the binding mode and system<br/>flexibility.<br/><br/>The CRA algorithm has been used to sample biological systems such<br/>as lysozyme L99A mutant, Bcr-Abl kinases and PDE5 phosphodiesterase<br/>and led to increased sampling of the backbone and more precise free energy<br/>results."]},{"key":"dc:format","label":"Dc Format","values":["text"]},{"key":"dc:title","label":"Title","values":["Modelling protein backbone loops using the Monte Carlo method"]}]}],"canonical_facts":{"dc:contributor.advisor":["Essex, Jonathan W."],"dc:creator":["Fernandez-Carmona, Juan"],"dc:date":["2009-04-03"],"dc:date.issued":["2009-04"],"dc:description.abstract":["Novel methods that perform local moves such as the gaussian bias or Con-<br/>certed Rotation with Angles, increase the exploration of the conformational<br/>phase space. These methods have been applied successfully to small systems,<br/>and have proved to be more efficient than the classical Monte Carlo method.<br/><br/>The main aim of my work was to study and include backbone moves<br/>for proteins, such as the Concerted Rotation with Angle (CRA) and the<br/>gaussian bias in the ProtoMS package. The CRA was then applied to several<br/>systems of biological interest to compute relative binding free energies and<br/>conformational changes to obtain insights into the binding mode and system<br/>flexibility.<br/><br/>The CRA algorithm has been used to sample biological systems such<br/>as lysozyme L99A mutant, Bcr-Abl kinases and PDE5 phosphodiesterase<br/>and led to increased sampling of the backbone and more precise free energy<br/>results."],"dc:format":["text"],"dc:identifier.uri":["https://eprints.soton.ac.uk/173851/1/FERNANDEZ_CARMONA_Juan.pdf"],"dc:publisher.department":["Chemistry (pre 2011 reorg)","School of Chemistry"],"dc:publisher.institution":["University of Southampton"],"dc:relation.isreferencedby":["https://eprints.soton.ac.uk/173851/"],"dc:title":["Modelling protein backbone loops using the Monte Carlo method"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["doctoral"],"dc:type.qualificationname":["Ph.D."]},"updated_at":"2026-07-24T04:36:21Z"}