Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking

We propose a flexible docking simulation based on parallel cascade selection molecular dynamics (PaCS-MD) as a post-processing treatment after a rigid docking simulation. PaCS-MD has been proposed as an enhanced sampling method for generating structural transition pathways from a given reactant to a...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Journal of molecular graphics & modelling 2019-11, Vol.92, p.94-99
Hauptverfasser: Harada, Ryuhei, Yoshino, Ryunosuke, Nishizawa, Hiroaki, Shigeta, Yasuteru
Format: Artikel
Sprache:eng
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 99
container_issue
container_start_page 94
container_title Journal of molecular graphics & modelling
container_volume 92
creator Harada, Ryuhei
Yoshino, Ryunosuke
Nishizawa, Hiroaki
Shigeta, Yasuteru
description We propose a flexible docking simulation based on parallel cascade selection molecular dynamics (PaCS-MD) as a post-processing treatment after a rigid docking simulation. PaCS-MD has been proposed as an enhanced sampling method for generating structural transition pathways from a given reactant to a product. The PaCS-MD cycle consists of the following two steps: (1) selections of important initial structures and (2) their conformational resampling from the selected initial structures. By repeating the conformational resampling from the important initial structures, structural transitions from the reactant to the product are gradually promoted. In the present flexible docking simulation, decoys (protein complexes) are generated by the rigid docking simulation a priori and employed as products of PaCS-MD. Then PaCS-MD is applied to reproduce association processes to the decoys from a reactant (completely separated proteins). To judge whether PaCS-MD found the association processes or not, the root-mean-square deviation measured from decoy (RMSDdecoy) was defined and monitored during the PaCS-MD cycles. By checking the RMSDdecoy values, a set of decoys is screened as a non-near native protein complex. In more detail, PaCS-MD detects near native protein complexes from the generated decoys by imposing a threshold (cutoff) for RMSDdecoy, i.e. RMSDdecoy 
doi_str_mv 10.1016/j.jmgm.2019.07.007
format Article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2265771482</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S1093326319303201</els_id><sourcerecordid>2265771482</sourcerecordid><originalsourceid>FETCH-LOGICAL-c356t-6ed7d760b2a4861708894ee53bce7a23be094be4f457af7cc619e5a0cdbbab493</originalsourceid><addsrcrecordid>eNp9kE1v1DAQhi1UREvhD3CofOwlYfyROJF6qaryIVWCA5wtf0wWL068tbOI_fd4tW2PnGYOz_tq5iHkA4OWAes_btvtvJlbDmxsQbUA6hW5YIMSjeRSnNUdRtEI3otz8raULQCIAdQbci6YkLKTwwX59d1kEyNG6kxxxiMtGNGtIS10TnXbR5OpPyxmDq7QNdHiMuJCp5TpLqcVw0JdmncR_2KhG1wwmxU9tQeawyZ46pP7HZbNO_J6MrHg-6d5SX5-uv9x96V5-Pb5693tQ-NE169Nj1551YPlRg49UzAMo0TshHWoDBcWYZQW5SQ7ZSblXM9G7Aw4b62xchSX5PrUW4973GNZ9RyKwxjNgmlfNOd9pxSTA68oP6Eup1IyTnqXw2zyQTPQR8N6q4-G9dGwBqWr4Rq6eurf2xn9S-RZaQVuTgDWL_8EzLq4gItDH3IVq30K_-v_B-48jwk</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2265771482</pqid></control><display><type>article</type><title>Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking</title><source>Elsevier ScienceDirect Journals Complete</source><creator>Harada, Ryuhei ; Yoshino, Ryunosuke ; Nishizawa, Hiroaki ; Shigeta, Yasuteru</creator><creatorcontrib>Harada, Ryuhei ; Yoshino, Ryunosuke ; Nishizawa, Hiroaki ; Shigeta, Yasuteru</creatorcontrib><description>We propose a flexible docking simulation based on parallel cascade selection molecular dynamics (PaCS-MD) as a post-processing treatment after a rigid docking simulation. PaCS-MD has been proposed as an enhanced sampling method for generating structural transition pathways from a given reactant to a product. The PaCS-MD cycle consists of the following two steps: (1) selections of important initial structures and (2) their conformational resampling from the selected initial structures. By repeating the conformational resampling from the important initial structures, structural transitions from the reactant to the product are gradually promoted. In the present flexible docking simulation, decoys (protein complexes) are generated by the rigid docking simulation a priori and employed as products of PaCS-MD. Then PaCS-MD is applied to reproduce association processes to the decoys from a reactant (completely separated proteins). To judge whether PaCS-MD found the association processes or not, the root-mean-square deviation measured from decoy (RMSDdecoy) was defined and monitored during the PaCS-MD cycles. By checking the RMSDdecoy values, a set of decoys is screened as a non-near native protein complex. In more detail, PaCS-MD detects near native protein complexes from the generated decoys by imposing a threshold (cutoff) for RMSDdecoy, i.e. RMSDdecoy &lt; cutoff. As a demonstration, the present flexible docking addressed dimerization processes of K48-linked ubiquitin dimer without a covalent bond between its monomers. Finally, PaCS-MD screened out non-near native protein complexes from decoys generated by a rigid docking simulation. [Display omitted] •PaCS-MD is a conformational sampling method for generating transitions from a given reactant to a product.•As a flexible docking simulation, PaCS-MD is combined with a rigid docking simulation.•As a product of PaCS-MD, decoys are generated by a rigid docking and PaCS-MD finds association processes to the decoys.•By confirming whether PaCS-MD finds association processes or not, one can screen out unreasonable decoys.</description><identifier>ISSN: 1093-3263</identifier><identifier>EISSN: 1873-4243</identifier><identifier>DOI: 10.1016/j.jmgm.2019.07.007</identifier><identifier>PMID: 31344548</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><ispartof>Journal of molecular graphics &amp; modelling, 2019-11, Vol.92, p.94-99</ispartof><rights>2019 Elsevier Inc.</rights><rights>Copyright © 2019 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c356t-6ed7d760b2a4861708894ee53bce7a23be094be4f457af7cc619e5a0cdbbab493</citedby><cites>FETCH-LOGICAL-c356t-6ed7d760b2a4861708894ee53bce7a23be094be4f457af7cc619e5a0cdbbab493</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jmgm.2019.07.007$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31344548$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Harada, Ryuhei</creatorcontrib><creatorcontrib>Yoshino, Ryunosuke</creatorcontrib><creatorcontrib>Nishizawa, Hiroaki</creatorcontrib><creatorcontrib>Shigeta, Yasuteru</creatorcontrib><title>Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking</title><title>Journal of molecular graphics &amp; modelling</title><addtitle>J Mol Graph Model</addtitle><description>We propose a flexible docking simulation based on parallel cascade selection molecular dynamics (PaCS-MD) as a post-processing treatment after a rigid docking simulation. PaCS-MD has been proposed as an enhanced sampling method for generating structural transition pathways from a given reactant to a product. The PaCS-MD cycle consists of the following two steps: (1) selections of important initial structures and (2) their conformational resampling from the selected initial structures. By repeating the conformational resampling from the important initial structures, structural transitions from the reactant to the product are gradually promoted. In the present flexible docking simulation, decoys (protein complexes) are generated by the rigid docking simulation a priori and employed as products of PaCS-MD. Then PaCS-MD is applied to reproduce association processes to the decoys from a reactant (completely separated proteins). To judge whether PaCS-MD found the association processes or not, the root-mean-square deviation measured from decoy (RMSDdecoy) was defined and monitored during the PaCS-MD cycles. By checking the RMSDdecoy values, a set of decoys is screened as a non-near native protein complex. In more detail, PaCS-MD detects near native protein complexes from the generated decoys by imposing a threshold (cutoff) for RMSDdecoy, i.e. RMSDdecoy &lt; cutoff. As a demonstration, the present flexible docking addressed dimerization processes of K48-linked ubiquitin dimer without a covalent bond between its monomers. Finally, PaCS-MD screened out non-near native protein complexes from decoys generated by a rigid docking simulation. [Display omitted] •PaCS-MD is a conformational sampling method for generating transitions from a given reactant to a product.•As a flexible docking simulation, PaCS-MD is combined with a rigid docking simulation.•As a product of PaCS-MD, decoys are generated by a rigid docking and PaCS-MD finds association processes to the decoys.•By confirming whether PaCS-MD finds association processes or not, one can screen out unreasonable decoys.</description><issn>1093-3263</issn><issn>1873-4243</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNp9kE1v1DAQhi1UREvhD3CofOwlYfyROJF6qaryIVWCA5wtf0wWL068tbOI_fd4tW2PnGYOz_tq5iHkA4OWAes_btvtvJlbDmxsQbUA6hW5YIMSjeRSnNUdRtEI3otz8raULQCIAdQbci6YkLKTwwX59d1kEyNG6kxxxiMtGNGtIS10TnXbR5OpPyxmDq7QNdHiMuJCp5TpLqcVw0JdmncR_2KhG1wwmxU9tQeawyZ46pP7HZbNO_J6MrHg-6d5SX5-uv9x96V5-Pb5693tQ-NE169Nj1551YPlRg49UzAMo0TshHWoDBcWYZQW5SQ7ZSblXM9G7Aw4b62xchSX5PrUW4973GNZ9RyKwxjNgmlfNOd9pxSTA68oP6Eup1IyTnqXw2zyQTPQR8N6q4-G9dGwBqWr4Rq6eurf2xn9S-RZaQVuTgDWL_8EzLq4gItDH3IVq30K_-v_B-48jwk</recordid><startdate>201911</startdate><enddate>201911</enddate><creator>Harada, Ryuhei</creator><creator>Yoshino, Ryunosuke</creator><creator>Nishizawa, Hiroaki</creator><creator>Shigeta, Yasuteru</creator><general>Elsevier Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>201911</creationdate><title>Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking</title><author>Harada, Ryuhei ; Yoshino, Ryunosuke ; Nishizawa, Hiroaki ; Shigeta, Yasuteru</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c356t-6ed7d760b2a4861708894ee53bce7a23be094be4f457af7cc619e5a0cdbbab493</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Harada, Ryuhei</creatorcontrib><creatorcontrib>Yoshino, Ryunosuke</creatorcontrib><creatorcontrib>Nishizawa, Hiroaki</creatorcontrib><creatorcontrib>Shigeta, Yasuteru</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of molecular graphics &amp; modelling</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Harada, Ryuhei</au><au>Yoshino, Ryunosuke</au><au>Nishizawa, Hiroaki</au><au>Shigeta, Yasuteru</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking</atitle><jtitle>Journal of molecular graphics &amp; modelling</jtitle><addtitle>J Mol Graph Model</addtitle><date>2019-11</date><risdate>2019</risdate><volume>92</volume><spage>94</spage><epage>99</epage><pages>94-99</pages><issn>1093-3263</issn><eissn>1873-4243</eissn><abstract>We propose a flexible docking simulation based on parallel cascade selection molecular dynamics (PaCS-MD) as a post-processing treatment after a rigid docking simulation. PaCS-MD has been proposed as an enhanced sampling method for generating structural transition pathways from a given reactant to a product. The PaCS-MD cycle consists of the following two steps: (1) selections of important initial structures and (2) their conformational resampling from the selected initial structures. By repeating the conformational resampling from the important initial structures, structural transitions from the reactant to the product are gradually promoted. In the present flexible docking simulation, decoys (protein complexes) are generated by the rigid docking simulation a priori and employed as products of PaCS-MD. Then PaCS-MD is applied to reproduce association processes to the decoys from a reactant (completely separated proteins). To judge whether PaCS-MD found the association processes or not, the root-mean-square deviation measured from decoy (RMSDdecoy) was defined and monitored during the PaCS-MD cycles. By checking the RMSDdecoy values, a set of decoys is screened as a non-near native protein complex. In more detail, PaCS-MD detects near native protein complexes from the generated decoys by imposing a threshold (cutoff) for RMSDdecoy, i.e. RMSDdecoy &lt; cutoff. As a demonstration, the present flexible docking addressed dimerization processes of K48-linked ubiquitin dimer without a covalent bond between its monomers. Finally, PaCS-MD screened out non-near native protein complexes from decoys generated by a rigid docking simulation. [Display omitted] •PaCS-MD is a conformational sampling method for generating transitions from a given reactant to a product.•As a flexible docking simulation, PaCS-MD is combined with a rigid docking simulation.•As a product of PaCS-MD, decoys are generated by a rigid docking and PaCS-MD finds association processes to the decoys.•By confirming whether PaCS-MD finds association processes or not, one can screen out unreasonable decoys.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>31344548</pmid><doi>10.1016/j.jmgm.2019.07.007</doi><tpages>6</tpages></addata></record>
fulltext fulltext
identifier ISSN: 1093-3263
ispartof Journal of molecular graphics & modelling, 2019-11, Vol.92, p.94-99
issn 1093-3263
1873-4243
language eng
recordid cdi_proquest_miscellaneous_2265771482
source Elsevier ScienceDirect Journals Complete
title Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T17%3A45%3A15IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Parallel%20cascade%20selection%20molecular%20dynamics%20to%20screen%20for%20protein%20complexes%20generated%20by%20rigid%20docking&rft.jtitle=Journal%20of%20molecular%20graphics%20&%20modelling&rft.au=Harada,%20Ryuhei&rft.date=2019-11&rft.volume=92&rft.spage=94&rft.epage=99&rft.pages=94-99&rft.issn=1093-3263&rft.eissn=1873-4243&rft_id=info:doi/10.1016/j.jmgm.2019.07.007&rft_dat=%3Cproquest_cross%3E2265771482%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2265771482&rft_id=info:pmid/31344548&rft_els_id=S1093326319303201&rfr_iscdi=true