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
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
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
Müsil, D., Zucić, D., Türk, V., Engh, R. A., Mayr, I., Huber, R., Popovic, T., Türk, V., Towatari, T., & Katunuma, N. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07771.x · Cited by 608
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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Energy landscapes in protein folding
Contessoto, V. G., & Onuchic, J. N. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-99507-8.00025-1 · Cited by 1
Protein structure similarity using recurrence relation technique
Somavarapu, J., Vani, K. S., & Kumar, K. P. (2015) · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) · doi:10.1109/cibcb.2015.7300329 · Cited by 1
Correlated rigid modes in protein families
Striegel, D. A., Wójtowicz, D., Przytycka, T. M., & Periwal, V. (2016) · Physical Biology · doi:10.1088/1478-3975/13/2/025003 · Cited by 1
A New Graph Theoretic Approach for Protein Threading
Song, Y., Qu, J., Xu, Y., & Cai, L. (2016) · Fundamenta Informaticae · doi:10.3233/fi-2016-1352 · Cited by 1
Prédiction de structures de macromolécules par apprentissage automatique
Alvarez, A. M. (2011) · Cited by 1
GRASP with Path-Relinking for the Maximum Contact Map Overlap Problem
Silva, R. M. A., Resende, M. G. C., Festa, P., Valentim, F. L., & Junior, F. N. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-09584-4_21 · Cited by 1
Protein sequence-structure alignment based on site-alignment probabilities.
Miyazawa, S. (2000) · PubMed · Cited by 1
VIRUS PARTICLE EXPLORER (VIPER): A REPOSITORY OF VIRUS CAPSID STRUCTURES
Reddy, V. S., Natarajan, P., Lander, G. C., Qu, C., Brooks, C. L., & Johnson, J. E. (2004) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789812562647_0020 · Cited by 1
Protein Fold Recognition Based on Distant Homologs
Sommer, I. (2007) · doi:10.1002/9783527619368.ch11 · Cited by 1
Novel knowledge-based potentials for ligand docking: variational approach to the old problem
Ruvinsky, A. M., & Kozintsev, A. V. (2004) · Biophysical Chemistry · doi:10.1016/j.bpc.2004.12.029 · Cited by 1
Effect of sidechain anisotropy on residue contact determination
Sun, W., & He, J. J. (2009) · IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) · doi:10.1109/bibmw.2009.5332123 · Cited by 1
A method for optimal design of a threading scoring function
Bienkowska, J. R., Rogers, R. G., & Smith, T. F. (1999) · Research in Computational Molecular Biology · doi:10.1145/299432.299446 · Cited by 1
Lobanov, M. Y., & Finkelshtein, A. (2009) · Molecular Biology · doi:10.1134/s0026893309040207 · Cited by 1
Knowledge-based interaction potentials for proteins
Rojnuckarin, A., & Subramaniam, S. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990701)36:1 · Cited by 59
Self-citationPathological and therapeutic antibodies: new tools for autoimmunity diagnosis and anticancer therapy
Tedesco, A. (2008) · Università degli Studi di Napoli Federico II · doi:10.6092/unina/fedoa/1959
Protein Structure Prediction By Threading: Force Field Philosophy, Approaches to Alignment
Huber, T., & Torda, A. E. (2001)
Self-Assembling of Local Searchers in Memetic Algorithms
Krasnogor, N., & Gustafson, S. (2006) · Springer eBooks · doi:10.1007/3-540-32363-5_11
Nishikawa, K. (2002) · Encyclopedia of Molecular Biology · doi:10.1002/047120918x.emb1545
The interfacial bioscience grand challenge.
Lane, P. D., Stevens, M. J., Jacobsen, R. B., Hong, J., Ayson, M. J., Crozier, P., Wood, N. L., Schoeniger, J. S., Kruppa, G. H., Sale, K. L., et al. (2004) · doi:10.2172/921141
Bayesian Segmentation using Residue Proximity for Secondary Structure and Contact Prediction
Bidargaddi, N. P., Chetty, M., & Kamruzzaman, J. (2006) · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) · doi:10.1109/cibcb.2006.331015
A Genetic Threading Method with Combined Structure- and Sequence-Based Information
Gu, J. F., & Wang, X. C. (2013) · Advanced materials research · doi:10.4028/www.scientific.net/amr.634-638.3930
Comprehensive statistical method for protein fold recognition
Bienkowska, J. R., Yu, L., Zarakhovich, S., Rogers, R. G., & Smith, T. F. (2000) · Research in Computational Molecular Biology · doi:10.1145/332306.332347
Directional adjacency-score function for protein fold recognition
Heo, M., Cheon, M., Kim, S., Chung, K., & Chang, I. (2009) · Interdisciplinary Bio Central · doi:10.4051/ibc.2009.1.0008
Optimisation of molecular function
Forst, C. V. (1999) · Birkhäuser Basel eBooks · doi:10.1007/978-3-0348-8817-2_22
Scoring Functions for Predicting Structure and Binding of Proteins
Dasgupta, B., & Liang, J. (2016) · doi:10.1002/9781119162254.ch02
Profile comparison revealed deviation from structural constraint at the positively selected sites
Oda, H., Ota, M., & Toh, H. (2016) · Biosystems · doi:10.1016/j.biosystems.2016.07.007
Time Algorithm for d-Dimensional Protein Folding in the HP-Model
Fu, B., & Wang, W. (2004)
A Visualization Tool to Evaluate Pairwise Protein Structure Alignment AlgorithmsPreprint
Bhattacharjee, S., & Mukhopadhyay, A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/342899
Eidhammer, I., Jonassen, I., & Taylor, W. R. (2003) · doi:10.1002/9780470092620.refs
Koliński, A., Godzik, A., & Skolnick, J. (2002) · Encyclopedia of Molecular Biology · doi:10.1002/047120918x.emb0308
Self-citationBastos, A. L. A., Lemos, R. P., Mariano, D., Yamada, C. A. O., Pirovani, M. M., & de Melo-Minardi, R. C. (2025) · Lecture notes in computer science · doi:10.1007/978-3-032-09336-3_13
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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