The DOI matches its Crossref record; 213 of the 213 references it cites were found in a registry or an index.
Integrative Structural Biology in the Era of Accurate Structure Prediction
Open accessAbstract
Characterizing the three-dimensional structure of macromolecules is central to understanding their function. Traditionally, structures of proteins and their complexes have been determined using experimental techniques such as X-ray crystallography, NMR, or cryo-electron microscopy-applied individually or in an integrative manner. Meanwhile, however, computational methods for protein structure prediction have been improving their accuracy, gradually, then suddenly, with the breakthrough advance by AlphaFold2, whose models of monomeric proteins are often as accurate as experimental structures. This breakthrough foreshadows a new era of computational methods that can build accurate models for most monomeric proteins. Here, we envision how such accurate modeling methods can combine with experimental structural biology techniques, enhancing integrative structural biology. We highlight the challenges that arise when considering multiple structural conformations, protein complexes, and polymorphic assemblies. These challenges will motivate further developments, both in modeling programs and in methods to solve experimental structures, towards better and quicker investigation of structure-function relationships.
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.
Integrity signals
Registry
Cites
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The programs were also shown to accurately assess their confidence at the level of individual residues and interdomain contacts (27,28,62).”
From AI-based structure prediction empowers integrative structural analysis of human nuclear pores (2022) · cites this paper as [62]
In the citing paper
“However, AlphaFold and RoseTTAfold have recently demonstrated unprecedented accuracy in predicting structures of monomeric proteins (27,28,(61)(62)(63)(64)(65)(66) and complexes (35,62,67,68).”
From AI-based structure prediction empowers integrative structural analysis of human nuclear pores (2022) · cites this paper as [62]
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
Items 201–213 of 213
Functional Amyloidogenesis and Cytotoxicity—Insights into Biology and Pathology
Fowler, D. M., & Kelly, J. W. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001459 · Cited by 17
Solution of the Phase Problem. I. The Centrosymmetric Crystalby H. Hauptman and J. Karle
ROGERS, D., & Wilson, A. J. C. (1955) · Acta Crystallographica · doi:10.1107/s0365110x55001230 · Cited by 16
Du, X., Wang, H., Zhu, Z., Zeng, X., Chang, Y., Zhang, J., Xing, E. P., & Xu, M. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab123 · Cited by 16
ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure
Narunsky, A., Nepomnyachiy, S., Ashkenazy, H., Kolodny, R., & Ben‐Tal, N. (2015) · Structure · doi:10.1016/j.str.2015.08.018 · Cited by 14
Self-citationFragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER
Richards, L. S., Millán, C., Miao, J., et al. (2020) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798320008049 · Cited by 14
The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP
Chojnowski, G., Sobolev, E. V., Heuser, P., & Lamzin, V. S. (2021) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798320016332 · Cited by 14
Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems
DiMaio, F. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7000-1_19 · Cited by 13
Phasertng: directed acyclic graphs for crystallographic phasing
McCoy, A. J., Stockwell, D. H., Sammito, M. D., Oeffner, R. D., Hatti, K. S., Croll, T. I., & Read, R. J. (2020) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798320014746 · Cited by 13
Design of novel granulopoietic proteins by topological rescaffolding
Alvarez, B. H., Skokowa, J., Coles, M. P., Mir, P., Nasri, M., Maksymenko, K., Weidmann, L., Rogers, K. W., Welte, K., Lupas, A. N., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000919 · Cited by 13
Self-citationWang, Y., Virtanen, J., Xue, Z., Tesmer, J. J. G., & Zhang, Y. (2016) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798316003016 · Cited by 11
Molecular-replacement phasing using predicted protein structures from AWSEM-Suite
Jin, S., Miller, M. D., Chen, M., Schafer, N. P., Lin, X., Chen, X., Phillips, G. N., & Wolynes, P. G. (2020) · IUCrJ · doi:10.1107/s2052252520013494 · Cited by 10
Matthews, L. H. (1955) · Nature · doi:10.1038/175915a0 · Cited by 1
McCafferty, C. L., Taylor, D. W., & Marcotte, E. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.14.426447 · Cited by 1
Flagged first, then by citations
Research works printed but not linked: 2
- Kinch, 2021, Topology Evaluation of Difficult Targets in the 14th Round of the Critical Assessment of Protein Structure Prediction (CASP14), Proteins: Struct. Funct. Bioinf.
- Demis Hassabis, Brief update on some exciting progress on #AlphaFold! We’ve been heads down working flat out on our full methods paper (currently under review) with accompanying open source code and on providing broad free access to AlphaFold for the scientific community. More very soon! https://t.co/uP7uzgGMSf, @demishassabis. (2021). https://twitter.com/demishassabis/status/1405922961710854144 (accessed June 23, 2021).
Cited by
Sorted by citations
AI-based structure prediction empowers integrative structural analysis of human nuclear pores
Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., Buczak, K., Schmidt, F. H., Margiotta, E., Mackmull, M.-T., et al. (2022) · Science · doi:10.1126/science.abm9506 · Cited by 355
AlphaFold2 Can Predict Single-Mutation Effects
McBride, J. M., Polev, K., Abdirasulov, A., Reinharz, V., Grzybowski, B. A., & Tlusty, T. (2023) · Physical Review Letters · doi:10.1103/physrevlett.131.218401 · Cited by 87
Lindorff-Larsen, K., & Kragelund, B. B. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167196 · Cited by 85
Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac118 · Cited by 32
Varadi, M., Bordin, N., Orengo, C., & Velankar, S. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102543 · Cited by 29
Metadata
- Authors
- Masrati, G., Landau, M., Ben-Tal, N., Lupas, A., Kosloff, M., & Kosinski, J.
- Affiliations
- Tel Aviv University (IL)
- Technion – Israel Institute of Technology (IL)
- Max Planck Institute for Developmental Biology (DE)
- University of Haifa (IL)
- Corresponding author
- Lupas, Andrei
- Kosloff, Mickey
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2021-10
- Volume
- 433
- Issue
- 20
- Pages
- 167127
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W3181374387
- Cited by
- 53
- References
- 213
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 8 · 2023: 9 · 2022: 21 · 2021: 7
- FWCI
- 1.18
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Molecular Biology (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Desy Publications Database (Deutsches Elektronen-Synchrotron DESY) (submittedVersion, other-oa)
- Funders
- Max-Planck-Gesellschaft
- Tel Aviv University
- Canadian Institutes of Health Research
- BMBF Berlin
- International Development Research Centre
- Azrieli Foundation (3512/19)
- Israel Science Foundation
- Bundesministerium für Bildung und Forschung (FKZ 031L0100)
- 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 › Receptor Mechanisms and Signaling
- Keywords
- integrative structural biology, protein structure prediction, AlphaFold2, macromolecular structure determination, protein complexes, structural polymorphism, structure-function relationship
- MeSH terms
- Animals, Humans, Models, Molecular, Protein Conformation, Proteins, Crystallography, X-Ray, Nuclear Magnetic Resonance, Biomolecular
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
