Academic Journal
Προβολή σε EDS

Martinize2 and Vermouth provide a unified framework for molecular topology generation.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Martinize2 and Vermouth provide a unified framework for molecular topology generation.
Συγγραφείς: Kroon, Peter C.1, Grünewald, Fabian1,2,3 Fabian.Gruenewald@h-its.org, Barnoud, Jonathan1,4, van Tilburg, Marco1, Brasnett, Chris1, Souza, Paulo C. T.1,5,6, Wassenaar, Tsjerk A.1, Marrink, Siewert J.1 s.j.marrink@rug.nl
Πηγή: eLife. 11/20/2025, Vol. 14, p1-30. 30p.
Θεματικοί όροι: *Molecular dynamics, *Software libraries (Computer programming), *Protein structure, *Simulation methods & models, *Biological systems
Περίληψη: Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design by high-throughput (HT) simulations is another forefront of MD. In these areas, the Martini coarse-grained force field, especially the latest version (i.e. v3), is being actively explored because it offers an enhanced spatial-temporal resolution. However, the automation tools for preparing simulations with the Martini force field, accompanying the previous version, were not designed for HT simulations or studies of complex cellular systems. Therefore, they become a major limiting factor. To address these shortcomings, we present the open-source Vermouth python library. Vermouth is designed to become the unified framework for developing programs, which prepare, run, and analyze Martini simulations of complex systems. To demonstrate the power of the Vermouth library, the Martinize2 program is showcased as a generalization of the martinize script, originally aimed to set up simulations of proteins. In contrast to the previous version, Martinize2 automatically handles protonation states in proteins and post-translation modifications, offers more options to fine-tune structural biases such as the elastic network (EN), and can convert non-protein molecules such as ligands. Finally, Martinize2 is used in two high-complexity benchmarks. The entire I-TASSER protein template database as well as a subset of 200,000 structures from the AlphaFold Protein Structure Database are converted to CG resolution and we illustrate how the checks on input structure quality can safeguard HT applications. [ABSTRACT FROM AUTHOR]
Βάση Δεδομένων: Academic Search Index
FullText Text:
  Availability: 0
CustomLinks:
  – Url: https://resolver.ebsco.com/c/fiv2js/result?sid=EBSCO:asx&genre=article&issn=2050084X&ISBN=&volume=14&issue=&date=20251120&spage=1&pages=1-30&title=eLife&atitle=Martinize2%20and%20Vermouth%20provide%20a%20unified%20framework%20for%20molecular%20topology%20generation.&aulast=Kroon%2C%20Peter%20C.&id=DOI:10.7554/eLife.90627
    Name: Full Text Finder (for New FTF UI) (ns324271)
    Category: fullText
    Text: Full Text Finder
    MouseOverText: Full Text Finder
Header DbId: asx
DbLabel: Academic Search Index
An: 189697402
RelevancyScore: 1393
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 1393.09375
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Martinize2 and Vermouth provide a unified framework for molecular topology generation.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Kroon%2C+Peter+C%2E%22">Kroon, Peter C.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Grünewald%2C+Fabian%22">Grünewald, Fabian</searchLink><relatesTo>1,2,3</relatesTo><i> Fabian.Gruenewald@h-its.org</i><br /><searchLink fieldCode="AR" term="%22Barnoud%2C+Jonathan%22">Barnoud, Jonathan</searchLink><relatesTo>1,4</relatesTo><br /><searchLink fieldCode="AR" term="%22van+Tilburg%2C+Marco%22">van Tilburg, Marco</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Brasnett%2C+Chris%22">Brasnett, Chris</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Souza%2C+Paulo+C%2E+T%2E%22">Souza, Paulo C. T.</searchLink><relatesTo>1,5,6</relatesTo><br /><searchLink fieldCode="AR" term="%22Wassenaar%2C+Tsjerk+A%2E%22">Wassenaar, Tsjerk A.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Marrink%2C+Siewert+J%2E%22">Marrink, Siewert J.</searchLink><relatesTo>1</relatesTo><i> s.j.marrink@rug.nl</i>
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22eLife%22">eLife</searchLink>. 11/20/2025, Vol. 14, p1-30. 30p.
– Name: Subject
  Label: Subject Terms
  Group: Su
  Data: *<searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br />*<searchLink fieldCode="DE" term="%22Software+libraries+%28Computer+programming%29%22">Software libraries (Computer programming)</searchLink><br />*<searchLink fieldCode="DE" term="%22Protein+structure%22">Protein structure</searchLink><br />*<searchLink fieldCode="DE" term="%22Simulation+methods+%26+models%22">Simulation methods & models</searchLink><br />*<searchLink fieldCode="DE" term="%22Biological+systems%22">Biological systems</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design by high-throughput (HT) simulations is another forefront of MD. In these areas, the Martini coarse-grained force field, especially the latest version (i.e. v3), is being actively explored because it offers an enhanced spatial-temporal resolution. However, the automation tools for preparing simulations with the Martini force field, accompanying the previous version, were not designed for HT simulations or studies of complex cellular systems. Therefore, they become a major limiting factor. To address these shortcomings, we present the open-source Vermouth python library. Vermouth is designed to become the unified framework for developing programs, which prepare, run, and analyze Martini simulations of complex systems. To demonstrate the power of the Vermouth library, the Martinize2 program is showcased as a generalization of the martinize script, originally aimed to set up simulations of proteins. In contrast to the previous version, Martinize2 automatically handles protonation states in proteins and post-translation modifications, offers more options to fine-tune structural biases such as the elastic network (EN), and can convert non-protein molecules such as ligands. Finally, Martinize2 is used in two high-complexity benchmarks. The entire I-TASSER protein template database as well as a subset of 200,000 structures from the AlphaFold Protein Structure Database are converted to CG resolution and we illustrate how the checks on input structure quality can safeguard HT applications. [ABSTRACT FROM AUTHOR]
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=asx&AN=189697402
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.7554/eLife.90627
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 30
        StartPage: 1
    Subjects:
      – SubjectFull: Molecular dynamics
        Type: general
      – SubjectFull: Software libraries (Computer programming)
        Type: general
      – SubjectFull: Protein structure
        Type: general
      – SubjectFull: Simulation methods & models
        Type: general
      – SubjectFull: Biological systems
        Type: general
    Titles:
      – TitleFull: Martinize2 and Vermouth provide a unified framework for molecular topology generation.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Kroon, Peter C.
      – PersonEntity:
          Name:
            NameFull: Grünewald, Fabian
      – PersonEntity:
          Name:
            NameFull: Barnoud, Jonathan
      – PersonEntity:
          Name:
            NameFull: van Tilburg, Marco
      – PersonEntity:
          Name:
            NameFull: Brasnett, Chris
      – PersonEntity:
          Name:
            NameFull: Souza, Paulo C. T.
      – PersonEntity:
          Name:
            NameFull: Wassenaar, Tsjerk A.
      – PersonEntity:
          Name:
            NameFull: Marrink, Siewert J.
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 20
              M: 11
              Text: 11/20/2025
              Type: published
              Y: 2025
          Identifiers:
            – Type: issn-print
              Value: 2050084X
          Numbering:
            – Type: volume
              Value: 14
          Titles:
            – TitleFull: eLife
              Type: main
ResultId 1