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From wireframes to immersive reality: a historical perspective on molecular visualization software.

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Title: From wireframes to immersive reality: a historical perspective on molecular visualization software.
Authors: Leitão AL; Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal., Enguita FJ; Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal.
Source: Briefings in bioinformatics [Brief Bioinform] 2026 Sep 01; Vol. 27 (5).
Publication Type: Journal Article; Review; Historical Article
Language: English
Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE
Imprint Name(s): Publication: Oxford : Oxford University Press
Original Publication: London ; Birmingham, AL : H. Stewart Publications, [2000-
MeSH Terms: Software*/history , Computational Biology*/methods , Computational Biology*/history , Computer Graphics*, History, 21st Century ; History, 20th Century ; Virtual Reality
Abstract: The evolution of molecular visualization software represents a pivotal yet often underappreciated dimension of computational structural biology and bioinformatics. As the scale and complexity of structural datasets increase, spanning from cryo-electron microscopy reconstructions to proteome-wide AI-predicted models, visualization tools have become essential for data interpretation, hypothesis generation, and effective scientific communication. Widely used platforms such as PyMOL, UCSF Chimera, and emerging virtual reality environments reflect decades of progressive innovation driven by advancements in computational hardware, graphics rendering, and algorithm development. This review traces the historical development of molecular graphics software, from early vector-based applications like FRODO and O, through interactive tools including RasMol and VMD, to modern real-time 3D visualization frameworks. We highlight key technological milestones and design principles that continue to shape contemporary software architectures, underscoring the interdisciplinary collaborations among chemists, structural biologists, and computer scientists that have propelled the field. Given the current integration of artificial intelligence, immersive visualization, and cloud computing in structural bioinformatics workflows, revisiting this topic provides critical context for guiding the design of more intuitive, scalable, and accessible visualization platforms. By documenting and critically analyzing this trajectory, the present work aims to honor the foundational contributions to molecular graphics while positioning the field as a dynamic and integral component of future bioinformatics research and computational discovery.
(© The Author(s) 2026. Published by Oxford University Press.)
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Contributed Indexing: Keywords: bioinformatics; graphical interface; molecular dynamics; molecular visualization
Entry Date(s): Date Created: 20260907 Date Completed: 20260907 Latest Revision: 20260909
Update Code: 20260909
PubMed Central ID: PMC13549435
DOI: 10.1093/bib/bbag373
PMID: 42704848
Database: MEDLINE
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PubTypeId: academicJournal
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  Data: From wireframes to immersive reality: a historical perspective on molecular visualization software.
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  Data: Journal Article; Review; Historical Article
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  Data: The evolution of molecular visualization software represents a pivotal yet often underappreciated dimension of computational structural biology and bioinformatics. As the scale and complexity of structural datasets increase, spanning from cryo-electron microscopy reconstructions to proteome-wide AI-predicted models, visualization tools have become essential for data interpretation, hypothesis generation, and effective scientific communication. Widely used platforms such as PyMOL, UCSF Chimera, and emerging virtual reality environments reflect decades of progressive innovation driven by advancements in computational hardware, graphics rendering, and algorithm development. This review traces the historical development of molecular graphics software, from early vector-based applications like FRODO and O, through interactive tools including RasMol and VMD, to modern real-time 3D visualization frameworks. We highlight key technological milestones and design principles that continue to shape contemporary software architectures, underscoring the interdisciplinary collaborations among chemists, structural biologists, and computer scientists that have propelled the field. Given the current integration of artificial intelligence, immersive visualization, and cloud computing in structural bioinformatics workflows, revisiting this topic provides critical context for guiding the design of more intuitive, scalable, and accessible visualization platforms. By documenting and critically analyzing this trajectory, the present work aims to honor the foundational contributions to molecular graphics while positioning the field as a dynamic and integral component of future bioinformatics research and computational discovery.<br /> (© The Author(s) 2026. Published by Oxford University Press.)
– Name: Ref
  Label: References
  Group: RefInfo
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  Data: <i>Keywords: </i>bioinformatics; graphical interface; molecular dynamics; molecular visualization
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  Data: <i>Date Created: </i>20260907 <i>Date Completed: </i>20260907 <i>Latest Revision: </i>20260909
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  Data: 10.1093/bib/bbag373
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        Value: 10.1093/bib/bbag373
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      – Code: eng
        Text: English
    Subjects:
      – SubjectFull: History, 21st Century
        Type: general
      – SubjectFull: History, 20th Century
        Type: general
      – SubjectFull: Virtual Reality
        Type: general
      – SubjectFull: Software history
        Type: general
      – SubjectFull: Computational Biology methods
        Type: general
      – SubjectFull: Computational Biology history
        Type: general
      – SubjectFull: Computer Graphics
        Type: general
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      – TitleFull: From wireframes to immersive reality: a historical perspective on molecular visualization software.
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            NameFull: Leitão AL
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            NameFull: Enguita FJ
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            – D: 01
              M: 09
              Text: 2026 Sep 01
              Type: published
              Y: 2026
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              Value: 1477-4054
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              Value: 27
            – Type: issue
              Value: 5
          Titles:
            – TitleFull: Briefings in bioinformatics
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