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Within this field, computational virology is becoming an indispensable pillar, serving as a \u201ccomputational microscope\u201d that bridges the spatio-temporal scales of viral processes, from individual protein dynamics to capsid assembly and cellular entry. This perspective article offers a critical overview of the current state, challenges, and future directions of computational approaches in physical virology. Our vision is anchored in the research presented at the 2025 EMBO\/FEBS Lecture Course on Physical Virology held in Sant Feliu de Guixols, Spain, and complemented by a targeted survey among attendees. We survey the principal methodological frameworks in use, from all-atom to multiscale molecular simulations, mesoscale simulations, and growing integration of artificial intelligence (AI) tools. We also critically examine the central obstacles impeding the field\u2019s progress, including the computational-experimental gap, limited accessibility to simulation data, reproducibility concerns, and systemic gender and geographic inequities. Finally, we outline future perspectives, proposing that integrating physics-aware AI with multiscale simulation frameworks, combined with community-driven data-sharing initiatives, will transform the computational microscope from a descriptive tool into a predictive engine for antiviral therapies, rational vaccine design, and biotechnological innovation.<\/jats:p>","DOI":"10.1093\/femsre\/fuag050","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T11:35:58Z","timestamp":1790076958000},"source":"Crossref","is-referenced-by-count":0,"title":["Computational methods in physical virology: a critical perspective across lengths and timescales"],"prefix":"10.1093","volume":"50","author":[{"given":"Adolfo B","family":"Poma","sequence":"first","affiliation":[{"name":"Institute of Fundamental Technological Research, Polish Academy of Sciences, ul. Pawin\u0301skiego 5B Department of Biosystems and Soft Matter, , 02-106 Warsaw ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis F","family":"Cofas-Vargas","sequence":"additional","affiliation":[{"name":"Universidad Aut\u00f3noma Metropolitana-Iztapalapa Departamento de Qu\u00edmica, , 09310 Mexico City C.P. ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando L","family":"Barroso\u00a0da\u00a0Silva","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences at Ribeir\u00e3o Preto, University of S\u00e3o Paulo Department of Biomolecular Sciences, , 14040-900 Ribeir\u00e3o Preto, S\u00e3o Paulo ,","place":["Brazil"]},{"name":"North Carolina State University Department of Chemical and Biomolecular Engineering, , 27695 Raleigh, North Carolina ,","place":["United 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