CoChat
Sign Up
Cited by 511Protein Structure and DynamicsEnzyme Structure and FunctionMachine Learning in Bioinformatics

The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.

AlphaFill: enriching AlphaFold models with ligands and cofactors

Open access
Hekkelman, Maarten L., de Vries, Ida, Joosten, Robbie P., Perrakis, Anastassis·2023·Nature Methods
DOI 10.1038/s41592-022-01685-yPMC PMC9911346

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Artificial intelligence-based protein structure prediction approaches have had a transformative effect on biomolecular sciences. The predicted protein models in the AlphaFold protein structure database, however, all lack coordinates for small molecules, essential for molecular structure or function: hemoglobin lacks bound heme; zinc-finger motifs lack zinc ions essential for structural integrity and metalloproteases lack metal ions needed for catalysis. Ligands important for biological function are absent too; no ADP or ATP is bound to any of the ATPases or kinases. Here we present AlphaFill, an algorithm that uses sequence and structure similarity to ‘transplant’ such ‘missing’ small molecules and ions from experimentally determined structures to predicted protein models. The algorithm was successfully validated against experimental structures. A total of 12,029,789 transplants were performed on 995,411 AlphaFold models and are available together with associated validation metrics in the alphafill.eu databank, a resource to help scientists make new hypotheses and design targeted experiments.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41592-022-01685-y

Cites

7 of 7 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 47

  1. Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000). · DOI
  2. Perrakis, A. & Sixma, T. K. AI revolutions in biology. EMBO Rep. 22, e54046 (2021). · DOI · Paper page
  3. van Beusekom, B. et al. Homology-based hydrogen bond information improves crystallographic structures in the PDB. Protein Sci. 27, 798–808 (2018). · DOI
  4. Fischer, J. D., Holliday, G. L. & Thornton, J. M. The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics 26, 2496–2497 (2010). · DOI
  5. Burley, S. K. et al. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 47, D520–D528 (2019). · DOI · Paper page
  6. Hanson, A. J. The quaternion-based spatial-coordinate and orientation-frame alignment problems. Acta. Cryst. A. 76, 432–457 (2020). · DOI
  7. PDBe-KB consortium. PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48, D344–D353 (2020). · DOI
  8. Krieger, E. & Vriend, G. YASARA View—molecular graphics for all devices—from smartphones to workstations. Bioinformatics 30, 2981–2982 (2014). · DOI
  9. Tukey, J. W. Exploratory Data Analysis (Addison-Wesley, 1977).
  10. The UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49, D480–D489 (2021). · DOI · Paper page
  11. Sehnal, D. et al. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49, W431–W437 (2021). · DOI · Paper page
  12. Chu, K. et al. Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin. Nature 403, 921–923 (2000). · DOI
  13. Nagao, S., Idomoto, A., Shibata, N., Higuchi, Y. & Hirota, S. Rational design of metal-binding sites in domain-swapped myoglobin dimers. J. Inorg. Biochem. 217, 111374 (2021). · DOI
  14. Torrance, J. W., MacArthur, M. W. & Thornton, J. M. Evolution of binding sites for zinc and calcium ions playing structural roles. Proteins 71, 813–830 (2008). · DOI
  15. Touw, W. G., van Beusekom, B., Evers, J. M. G., Vriend, G. & Joosten, R. P. Validation and correction of Zn–CysxHisy complexes. Acta Cryst. D. 72, 1110–1118 (2016). · DOI
  16. Davies, C. W., Paul, L. N., Kim, M.-I. & Das, C. Structural and thermodynamic comparison of the catalytic domain of AMSH and AMSH-LP: nearly identical fold but different stability. J. Mol. Biol. 413, 416–429 (2011). · DOI
  17. Bentley, M. L. et al. Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex. EMBO J. 30, 3285–3297 (2011). · DOI
  18. Tang, N. et al. Zinc finger protein 91 accelerates tumour progression by activating β-catenin signalling in pancreatic cancer. Cell Prolif. 54, e13031 (2021). · DOI
  19. Patel, A. et al. DNA conformation induces adaptable binding by tandem zinc finger proteins. Cell 173, 221–233.e12 (2018). · DOI
  20. Tian, Z. et al. Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms. Cell Discov. 6, 17 (2020). · DOI
  21. Stefan, C., Jansen, S. & Bollen, M. NPP-type ectophosphodiesterases: unity in diversity. Trends Biochem. Sci. 30, 542–550 (2005). · DOI
  22. Borza, R., Salgado-Polo, F., Moolenaar, W. H. & Perrakis, A. Structure and function of the ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family: tidying up diversity. J. Biol. Chem. 298, 101526 (2022). · DOI
  23. Levinson, N. M. et al. A Src-like inactive conformation in the Abl tyrosine kinase domain. PLoS Biol. 4, e144 (2006). · DOI
  24. Bagdonas, H., Fogarty, C. A., Fadda, E. & Agirre, J. The case for post-predictional modifications in the AlphaFold Protein Structure Database. Nat. Struct. Mol. Biol. 28, 869–870 (2021). · DOI
  25. Sander, C. & Schneider, R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56–68 (1991). · DOI
  26. van Beusekom, B. et al. LAHMA: structure analysis through local annotation of homology-matched amino acids. Acta. Cryst. D. 77, 28–40 (2021). · DOI
  27. Holm, L. in Structural Bioinformatics: Methods and Protocols (ed. Gáspári, Z.) 29–42 (Springer, 2020). · DOI
  28. Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst. D. 60, 2256–2268 (2004). · DOI
  29. Berbasova, T. et al. Rational design of a colorimetric pH sensor from a soluble retinoic acid chaperone. J. Am. Chem. Soc. 135, 16111–16119 (2013). · DOI
  30. Vaezeslami, S., Mathes, E., Vasileiou, C., Borhan, B. & Geiger, J. H. The structure of apo-wild-type cellular retinoic acid binding protein II at 1.4 Å and its relationship to ligand binding and nuclear translocation. J. Mol. Biol. 363, 687–701 (2006). · DOI
  31. Dennis, M. L. et al. Crystal structures of human ENPP1 in apo and bound forms. Acta Cryst. D. 76, 889–898 (2020). · DOI
  32. Gorelik, A., Randriamihaja, A., Illes, K. & Nagar, B. Structural basis for nucleotide recognition by the ectoenzyme CD203c. FEBS J. 285, 2481–2494 (2018). · DOI
  33. Albright, R. A. et al. Molecular basis of purinergic signal metabolism by ectonucleotide pyrophosphatase/phosphodiesterases 4 and 1 and implications in stroke. J. Biol. Chem. 289, 3294–3306 (2014). · DOI
  34. Gorelik, A., Randriamihaja, A., Illes, K. & Nagar, B. A key tyrosine substitution restricts nucleotide hydrolysis by the ectoenzyme NPP5. FEBS J. 284, 3718–3726 (2017). · DOI
  35. Morita, J. et al. Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase. Sci. Rep. 6, 20995 (2016). · DOI
  36. Gorelik, A., Liu, F., Illes, K. & Nagar, B. Crystal structure of the human alkaline sphingomyelinase provides insights into substrate recognition. J. Biol. Chem. 292, 7087–7094 (2017). · DOI
  37. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990). · DOI · Paper page
  38. Feng, Z. et al. Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20, 2153–2155 (2004). · DOI
  39. Hekkelman, M. L. & Vriend, G. MRS: a fast and compact retrieval system for biological data. Nucleic Acids Res. 33, W766–W769 (2005). · DOI
  40. Westbrook, J. D. et al. PDBx/mmCIF ecosystem: foundational semantic tools for structural biology. J. Mol. Biol. 434, 167599 (2022). · DOI
  41. Cowtan, KevinD. The Clipper C++ libraries for X-ray crystallography. IUCr Computing Commission Newsletter 2, 4–9 (2003).
  42. Feldman, S. I. Make—a program for maintaining computer programs. J. Softw. Pract. Exp. 9, 255–265 (1979). · DOI
  43. Joosten, R. P. et al. A series of PDB related databases for everyday needs. Nucleic Acids Res. 39, D411–D419 (2011). · DOI
  44. Stonebraker, M. & Rowe, L. A. The design of POSTGRES. SIGMOD Rec. 15, 340–355 (1986). · DOI
  45. Krieger, E. et al. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8. Proteins 77, 114–122 (2009). · DOI
  46. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta. Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010). · DOI · Paper page
  47. McNicholas, S., Potterton, E., Wilson, K. S. & Noble, M. E. M. Presenting your structures: the CCP4mg molecular-graphics software. Acta. Cryst. D. 67, 386–394 (2011). · DOI

Cited by

Sorted by citations

Metadata

Authors
Hekkelman, M. L., de Vries, I., Joosten, R. P., & Perrakis, A.
Affiliations
The Netherlands Cancer Institute (NL)
Corresponding author
Joosten, Robbie P.
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2022-11-24
Volume
20
Issue
2
Pages
205-213
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/s41592-022-01685-y
PMC
PMC9911346
OpenAlex
W4310058955
Cited by
511
References
7
Citations by year
2026: 99 · 2025: 117 · 2024: 160 · 2023: 107 · 2022: 28
FWCI
33.72
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Methods (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
EC | Horizon 2020 Framework Programme (871037)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords
AlphaFold, protein structure prediction, cofactors, metal ions, small molecule binding, structural similarity, sequence similarity, protein-ligand binding, protein structure database
MeSH terms
Artificial Intelligence, Ions, Ligands, Protein Conformation, Proteins, Zinc

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review