The DOI matches its Crossref record; 33 of the 34 references it cites were found in a registry or an index.
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 [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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Cites
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The protein data bank: A computer-based archival file for macromolecular structures
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A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure
Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991) · Science · doi:10.1126/science.1853201 · Cited by 2,851
Solvation energy in protein folding and binding
Eisenberg, D. S., & McLachlan, A. D. (1986) · Nature · doi:10.1038/319199a0 · Cited by 1,866
Tertiary templates for proteins
Ponder, J. W., & Richards, F. M. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90358-5 · Cited by 1,480
Profile analysis: detection of distantly related proteins.
Gribskov, M., McLachlan, A. D., & Eisenberg, D. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.13.4355 · Cited by 1,325
Calculation of conformational ensembles from potentials of mena force
Sippl, M. J. (1990) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80269-4 · Cited by 1,068
Selection of representative protein data sets
Hobohm, U., Scharf, M. E., Schneider, R., & Sander, C. (1992) · Protein Science · doi:10.1002/pro.5560010313 · Cited by 816
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Structure of oxidized poplar plastocyanin at 1·6 Å resolution
Guss, J. M., & Freeman, H. C. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80064-3 · Cited by 507
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1 of the 34 references couldn’t be matched to a known paper.
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Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169
Modeller: Generation and Refinement of Homology-Based Protein Structure Models
Fiser, A., & Šali, A. (2003) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(03)74020-8 · Cited by 1,708
Enhanced genome annotation using structural profiles in the program 3D-PSSM 1 1Edited by J. Thornton
Kelley, L. A., MacCallum, R. M., & Sternberg, M. J. E. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3741 · Cited by 1,464
Eddy, S. R. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80056-x · Cited by 1,445
Metadata
- 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
- 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
- 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
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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.
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