Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold
The human reference proteome is routinely modelled with predictive tools such as AlphaFold2. We recently released a database in which, for each human protein, the AlphaFold2 model is paired with its ESMFold counterpart. The two predictive methods take advantage of different procedures and it is inte...
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Elsevier
2025-06-01
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| Series: | Current Research in Structural Biology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2665928X25000042 |
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| author | Matteo Manfredi Castrense Savojardo Pier Luigi Martelli Rita Casadio |
| author_facet | Matteo Manfredi Castrense Savojardo Pier Luigi Martelli Rita Casadio |
| author_sort | Matteo Manfredi |
| collection | DOAJ |
| description | The human reference proteome is routinely modelled with predictive tools such as AlphaFold2. We recently released a database in which, for each human protein, the AlphaFold2 model is paired with its ESMFold counterpart. The two predictive methods take advantage of different procedures and it is interesting to compare them in relation to their quality, particularly when an experimental protein structure is not available. Here, we select three state-of-the-art quality assessment methods and we adopt them to compare 42,942 pairs of models. This procedure helps to find the most reliable models for human proteins, particularly for the set of proteins for which structure prediction methods give dissimilar results. We obtain that when predicted structures are similar, AlphaFold2 models consistently receive higher scores than the ESMFold counterparts. When predicted structures differ, the ESMFold model is the best choice for 49 % of the proteins according to a consensus of the three QA tools. |
| format | Article |
| id | doaj-art-a50bd6f975434d00bf8d8cd18be93be7 |
| institution | DOAJ |
| issn | 2665-928X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Research in Structural Biology |
| spelling | doaj-art-a50bd6f975434d00bf8d8cd18be93be72025-08-20T02:39:37ZengElsevierCurrent Research in Structural Biology2665-928X2025-06-01910016710.1016/j.crstbi.2025.100167Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFoldMatteo Manfredi0Castrense Savojardo1Pier Luigi Martelli2Rita Casadio3Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, ItalyBiocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy; Corresponding author.Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy; Biocomputing Group, AlmaClimate Interdepartmental Center, University of Bologna, Italy; Institute of Biomembrane and Bioenergetics, Italian National Research Council (IBIOM-CNR), ItalyBiocomputing Group, AlmaClimate Interdepartmental Center, University of Bologna, Italy; Institute of Biomembrane and Bioenergetics, Italian National Research Council (IBIOM-CNR), Italy; Corresponding author. Biocomputing Group, AlmaClimate Interdepartmental Center, University of Bologna, Italy.The human reference proteome is routinely modelled with predictive tools such as AlphaFold2. We recently released a database in which, for each human protein, the AlphaFold2 model is paired with its ESMFold counterpart. The two predictive methods take advantage of different procedures and it is interesting to compare them in relation to their quality, particularly when an experimental protein structure is not available. Here, we select three state-of-the-art quality assessment methods and we adopt them to compare 42,942 pairs of models. This procedure helps to find the most reliable models for human proteins, particularly for the set of proteins for which structure prediction methods give dissimilar results. We obtain that when predicted structures are similar, AlphaFold2 models consistently receive higher scores than the ESMFold counterparts. When predicted structures differ, the ESMFold model is the best choice for 49 % of the proteins according to a consensus of the three QA tools.http://www.sciencedirect.com/science/article/pii/S2665928X25000042Human protein structure predictionAI computed structural modelsStructural model quality assessmentModel secondary structureModel solvent accessibilityAlphaFold2 |
| spellingShingle | Matteo Manfredi Castrense Savojardo Pier Luigi Martelli Rita Casadio Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold Current Research in Structural Biology Human protein structure prediction AI computed structural models Structural model quality assessment Model secondary structure Model solvent accessibility AlphaFold2 |
| title | Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold |
| title_full | Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold |
| title_fullStr | Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold |
| title_full_unstemmed | Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold |
| title_short | Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold |
| title_sort | evaluation of the structural models of the human reference proteome alphafold2 versus esmfold |
| topic | Human protein structure prediction AI computed structural models Structural model quality assessment Model secondary structure Model solvent accessibility AlphaFold2 |
| url | http://www.sciencedirect.com/science/article/pii/S2665928X25000042 |
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