Normal mode-guided transition pathway generation in proteins
Publication Date
October 11, 2017
Authors
Byung Ho Lee, Sangjae Seo, Min Hyeok Kim, Youngjin Kim, et al
Volume
12
Issue
10
Pages
e0185658
DOI
https://dx.plos.org/10.1371/journal.pone.0185658
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0185658
Scopus
85031017657
Mendeley
http://www.mendeley.com/research/normal-modeguided-transition-pathway-generation-proteins
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"Normal mode-guided transition pathway generation in proteins", "type"=>"journal", "authors"=>[{"first_name"=>"Byung Ho", "last_name"=>"Lee", "scopus_author_id"=>"56599325400"}, {"first_name"=>"Sangjae", "last_name"=>"Seo", "scopus_author_id"=>"36350296100"}, {"first_name"=>"Min Hyeok", "last_name"=>"Kim", "scopus_author_id"=>"57189018093"}, {"first_name"=>"Youngjin", "last_name"=>"Kim", "scopus_author_id"=>"56337405000"}, {"first_name"=>"Soojin", "last_name"=>"Jo", "scopus_author_id"=>"56039266000"}, {"first_name"=>"Moon ki", "last_name"=>"Choi", "scopus_author_id"=>"57196022565"}, {"first_name"=>"Hoomin", "last_name"=>"Lee", "scopus_author_id"=>"56267844600"}, {"first_name"=>"Jae Boong", "last_name"=>"Choi", "scopus_author_id"=>"24402894300"}, {"first_name"=>"Moon Ki", "last_name"=>"Kim", "scopus_author_id"=>"34975445300"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1111111111", "doi"=>"10.1371/journal.pone.0185658", "pui"=>"618698376", "issn"=>"19326203", "sgr"=>"85031017657", "scopus"=>"2-s2.0-85031017657"}, "id"=>"2ce7b030-a147-3d78-acee-800a5f39cfa5", "abstract"=>"© 2017 Lee et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI) that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this.", "link"=>"http://www.mendeley.com/research/normal-modeguided-transition-pathway-generation-proteins", "reader_count"=>4, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Other"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Other"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Unspecified"=>{"Unspecified"=>3}}, "group_count"=>1}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85031017657"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85031017657?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85031017657&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=85031017657&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/85031017657", "dc:identifier"=>"SCOPUS_ID:85031017657", "eid"=>"2-s2.0-85031017657", "dc:title"=>"Normal mode-guided transition pathway generation in proteins", "dc:creator"=>"Lee B.", "prism:publicationName"=>"PLoS ONE", "prism:eIssn"=>"19326203", "prism:volume"=>"12", "prism:issueIdentifier"=>"10", "prism:pageRange"=>nil, "prism:coverDate"=>"2017-10-01", "prism:coverDisplayDate"=>"October 2017", "prism:doi"=>"10.1371/journal.pone.0185658", "citedby-count"=>"1", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"Sungkyunkwan University", "affiliation-city"=>"Jongno-gu", "affiliation-country"=>"South Korea"}], "pubmed-id"=>"29020017", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e0185658", "source-id"=>"10600153309", "openaccess"=>"1", "openaccessFlag"=>true}

Counter

  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"63", "xml_views"=>"6", "html_views"=>"151"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"113"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"16", "xml_views"=>"1", "html_views"=>"136"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"13", "xml_views"=>"1", "html_views"=>"35"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"40", "xml_views"=>"2", "html_views"=>"22"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"15", "xml_views"=>"2", "html_views"=>"22"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"18"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"18", "xml_views"=>"1", "html_views"=>"24"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"4", "html_views"=>"14"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"12", "xml_views"=>"2", "html_views"=>"34"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"36"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"25"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"34"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"19"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"18"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"15"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"13"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"15"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"22"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"26", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"17"}

PMC Usage Stats

  • {"unique-ip"=>"24", "full-text"=>"6", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"19", "full-text"=>"14", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"2", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"10", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
Loading … Spinner
There are currently no alerts