Topology fingerprint approach to the inverse protein folding problem
Abstract
We describe the most general solution to date of the problem of matching globular protein sequences to the appropriate three-dimensional structures. The screening template, against which sequences are tested, is provided by a protein "structural fingerprint" library based on the contact map and the buried/exposed pattern of residues. Then, a lattice Monte Carlo algorithm validates or dismisses the stability of the proposed fold. Examples of known structural similarities between proteins having weakly or unrelated sequences such as the globins and phycocyanins, the eight-member alpha/beta fold of triose phosphate isomerase and even a close structural equivalence between azurin and immunoglobulins are found.
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The domains presented were the consensus of folds identified by Composer, MatchMaker, GeneFold, Robetta, Fugue, and Swiss-Model.
“The domains presented were the consensus of folds identified by Composer [53], MatchMaker [54], GeneFold [55], Robetta [56], Fugue [57], and Swiss-Model [58].”
From Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007) · cites this paper as [54]
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- Authors
- Godzik, A., Kolinski, A., & Skolnick, J.
- Affiliations
- Scripps Research Institute (US)
- Corresponding author
- Skolnick, Jeffrey
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1992-09
- Volume
- 227
- Issue
- 1
- Pages
- 227-238
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2040594319
- Cited by
- 339
- References
- 34
- Citations by year
- 2025: 3 · 2022: 2 · 2021: 1 · 2020: 3 · 2018: 3 · 2017: 2 · 2016: 5 · 2015: 3 · 2014: 6 · 2013: 4 · 2012: 2
- FWCI
- 7.82
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM 37408, R01GM037408)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- inverse protein folding, protein structure prediction, structural fingerprints, contact maps, lattice Monte Carlo simulation, globin, phycocyanin, triosephosphate isomerase, azurin, immunoglobulins, structural equivalence
- MeSH terms
- Algorithms, Azurin, Bacterial Outer Membrane Proteins, Bacterial Proteins, Globins, Immunoglobulin lambda-Chains, Models, Molecular, Phycocyanin, Plant Proteins, Plastocyanin, Protein Conformation, Structure-Activity Relationship, Thermodynamics, Databases, Factual, Sequence Alignment
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 ›
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