Analysing protein complexes in plant science: insights and limitation with AlphaFold 3
Abstract AlphaFold 3 (AF3), an artificial intelligence (AI)-based software for protein complex structure prediction, represents a significant advancement in structural biology. Its flexibility and enhanced scalability have unlocked new applications in various fields, specifically in plant science, i...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
SpringerOpen
2025-05-01
|
| Series: | Botanical Studies |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40529-025-00462-2 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850270714098089984 |
|---|---|
| author | Pei-Yu Lin Shiang-Chin Huang Kuan-Lin Chen Yu-Chun Huang Chia-Yu Liao Guan-Jun Lin HueyTyng Lee Pao-Yang Chen |
| author_facet | Pei-Yu Lin Shiang-Chin Huang Kuan-Lin Chen Yu-Chun Huang Chia-Yu Liao Guan-Jun Lin HueyTyng Lee Pao-Yang Chen |
| author_sort | Pei-Yu Lin |
| collection | DOAJ |
| description | Abstract AlphaFold 3 (AF3), an artificial intelligence (AI)-based software for protein complex structure prediction, represents a significant advancement in structural biology. Its flexibility and enhanced scalability have unlocked new applications in various fields, specifically in plant science, including improving crop resilience and predicting the structures of plant-specific proteins involved in stress responses, signalling pathways, and immune responses. Comparisons with existing tools, such as ClusPro and AlphaPulldown, highlight AF3’s unique strengths in sequence-based interaction predictions and its greater adaptability to various biomolecular structures. However, limitations persist, including challenges in modelling large complexes, protein dynamics, and structures from underrepresented plant proteins with limited evolutionary data. Additionally, AF3 encounters difficulties in predicting mutation effects on protein interactions and DNA binding, which can be improved with molecular dynamics and experimental validation. This review presents an overview of AF3’s advancements, using examples in plant and fungal research, and comparisons with existing tools. It also discusses current limitations and offers perspectives on integrating molecular dynamics and experimental validation to enhance its capabilities. |
| format | Article |
| id | doaj-art-3e036c25463348fda62d8097f923fa13 |
| institution | OA Journals |
| issn | 1999-3110 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Botanical Studies |
| spelling | doaj-art-3e036c25463348fda62d8097f923fa132025-08-20T01:52:29ZengSpringerOpenBotanical Studies1999-31102025-05-0166111210.1186/s40529-025-00462-2Analysing protein complexes in plant science: insights and limitation with AlphaFold 3Pei-Yu Lin0Shiang-Chin Huang1Kuan-Lin Chen2Yu-Chun Huang3Chia-Yu Liao4Guan-Jun Lin5HueyTyng Lee6Pao-Yang Chen7Institute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaAbstract AlphaFold 3 (AF3), an artificial intelligence (AI)-based software for protein complex structure prediction, represents a significant advancement in structural biology. Its flexibility and enhanced scalability have unlocked new applications in various fields, specifically in plant science, including improving crop resilience and predicting the structures of plant-specific proteins involved in stress responses, signalling pathways, and immune responses. Comparisons with existing tools, such as ClusPro and AlphaPulldown, highlight AF3’s unique strengths in sequence-based interaction predictions and its greater adaptability to various biomolecular structures. However, limitations persist, including challenges in modelling large complexes, protein dynamics, and structures from underrepresented plant proteins with limited evolutionary data. Additionally, AF3 encounters difficulties in predicting mutation effects on protein interactions and DNA binding, which can be improved with molecular dynamics and experimental validation. This review presents an overview of AF3’s advancements, using examples in plant and fungal research, and comparisons with existing tools. It also discusses current limitations and offers perspectives on integrating molecular dynamics and experimental validation to enhance its capabilities.https://doi.org/10.1186/s40529-025-00462-2AlphaFold 3Crop resilienceProtein structureProtein–protein interactionProtein complexStructure biology |
| spellingShingle | Pei-Yu Lin Shiang-Chin Huang Kuan-Lin Chen Yu-Chun Huang Chia-Yu Liao Guan-Jun Lin HueyTyng Lee Pao-Yang Chen Analysing protein complexes in plant science: insights and limitation with AlphaFold 3 Botanical Studies AlphaFold 3 Crop resilience Protein structure Protein–protein interaction Protein complex Structure biology |
| title | Analysing protein complexes in plant science: insights and limitation with AlphaFold 3 |
| title_full | Analysing protein complexes in plant science: insights and limitation with AlphaFold 3 |
| title_fullStr | Analysing protein complexes in plant science: insights and limitation with AlphaFold 3 |
| title_full_unstemmed | Analysing protein complexes in plant science: insights and limitation with AlphaFold 3 |
| title_short | Analysing protein complexes in plant science: insights and limitation with AlphaFold 3 |
| title_sort | analysing protein complexes in plant science insights and limitation with alphafold 3 |
| topic | AlphaFold 3 Crop resilience Protein structure Protein–protein interaction Protein complex Structure biology |
| url | https://doi.org/10.1186/s40529-025-00462-2 |
| work_keys_str_mv | AT peiyulin analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 AT shiangchinhuang analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 AT kuanlinchen analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 AT yuchunhuang analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 AT chiayuliao analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 AT guanjunlin analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 AT hueytynglee analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 AT paoyangchen analysingproteincomplexesinplantscienceinsightsandlimitationwithalphafold3 |