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
Protein database searches for multiple alignments.
Altschul, S. F., & Lipman, D. J. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.14.5509 · Cited by 483
Richards, F. M., & Kundrot, C. E. (1988) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340030202 · Cited by 400
The evolution of α/β barrel enzymes
Farber, G. K., & Petsko, G. A. (1990) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(90)90035-a · Cited by 380
Baker, E. N. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90129-5 · Cited by 362
Simulations of the Folding of a Globular Protein
Skolnick, J., & Koliński, A. (1990) · Science · doi:10.1126/science.250.4984.1121 · Cited by 314
Self-citationIdentification of protein sequence homology by consensus template alignment
Taylor, W. R. (1986) · Journal of Molecular Biology · doi:10.1016/0022-2836(86)90308-6 · Cited by 280
Evolution of CuZn superoxide dismutase and the Greek Key β‐barrel structural motif
Getzoff, E. D., Tainer, J. A., Stempien, M. M., Bell, G. I., & Hallewell, R. A. (1989) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340050408 · Cited by 209
General methods of sequence comparison
Waterman, M. S. (1984) · Bulletin of Mathematical Biology · doi:10.1016/s0092-8240(84)80054-3 · Cited by 208
Structural models of the redox centres in cytochrome oxidase.
Holm, L., Saraste, M., & Wikström, M. K. F. (1987) · The EMBO Journal · doi:10.1002/j.1460-2075.1987.tb02578.x · Cited by 204
A sensitive procedure to compare amino acid sequences
Argos, P. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90226-9 · Cited by 190
Skolnick, J., & Koliński, A. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)80070-b · Cited by 166
Self-citationTertiary Structure of Proteins. I. : Representation and Computation of the Conformations
Nishikawa, K., Ooi, T., Isogai, Y., & Saitō, N. (1972) · Journal of the Physical Society of Japan · doi:10.1143/jpsj.32.1331 · Cited by 136
A search for the most stable folds of protein chains
Finkelstein, A. V., & Reva, B. A. (1991) · Nature · doi:10.1038/351497a0 · Cited by 135
Evolution of proteins formed by β-sheets
Chothia, C., & Lesk, A. M. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90178-4 · Cited by 128
Structure of a novel bence-jones protein (Rhe) fragment at 1·6 Å resolution
Furey, W. S., Wang, B. C., Yoo, C. S., Sax, M., & Huber, R. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80104-1 · Cited by 117
Computer Simulations of Globular Protein Folding and Tertiary Structure
Skolnick, J., & Koliński, A. (1989) · Annual Review of Physical Chemistry · doi:10.1146/annurev.pc.40.100189.001231 · Cited by 98
Self-citationA 2.0-Å structure of the blue copper protein (cupredoxin) from Alcaligenes faecalis S-6
Adman, E. T., Turley, S., Bramson, R., Petratos, K., Banner, D. W., Tsernoglou, D., Beppu, T., & Watanabe, H. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31227-9 · Cited by 96
Comparison of the structures of globins and phycocyanins: Evidence for evolutionary relationship
Pastore, A., & Lesk, A. M. (1990) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340080204 · Cited by 95
Prediction of progress at last
Thornton, J. M., Flores, T. P., Jones, D. T., & Swindells, M. B. (1991) · Nature · doi:10.1038/354105a0 · Cited by 74
The development of crystallographic enzymology.
Dc, P. (1970) · PubMed · Cited by 48
Kawula, T. H., Spinota, S. M., Klapper, D. G., & Cannon, J. G. (1987) · Molecular Microbiology · doi:10.1111/j.1365-2958.1987.tb00510.x · Cited by 39
Conservation of residue interactions in a family of Ca-binding proteins
Godzik, A., & Sander, C. (1989) · Protein Engineering Design and Selection · doi:10.1093/protein/2.8.589 · Cited by 37
Self-citationThe structural homology of amicyanin from Thiobacillus versutus to plant plastocyanins.
BEEUMEN, J. V., Bun, S. V., Canters, G. W., Lommen, A., & Chothia, C. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)67729-x · Cited by 25
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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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