Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
Open accessAbstract
The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging from the many genome projects. To this end, fold assignment, comparative protein structure modeling, and model evaluation were automated completely. As an illustration, the method was applied to the proteins in the Saccharomyces cerevisiae (baker’s yeast) genome. It resulted in all-atom 3D models for substantial segments of 1,071 (17%) of the yeast proteins, only 40 of which have had their 3D structure determined experimentally. Of the 1,071 modeled yeast proteins, 236 were related clearly to a protein of known structure for the first time; 41 of these previously have not been characterized at all.
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YNL181w encodes a putative oxidoreductase that localizes to the ER and ynl181w hypomorphic mutants showed altered sensitivities to numerous bioactive compounds.
“Indeed, YNL181w encodes a putative oxidoreductase that localizes to the ER (27) and, consistent with defective membrane function, ynl181w hypomorphic mutants showed altered sensitivities to numerous bioactive compounds (fig. S18)(8).”
From A global genetic interaction network maps a wiring diagram of cellular function (2016) · cites this paper as [27]
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The relation between the divergence of sequence and structure in proteins.
Chothia, C., & Lesk, A. M. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04288.x · Cited by 2,458 · see citing works
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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 · see citing works
Self-citationThe Genomic Landscapes of Human Breast and Colorectal Cancers
Wood, L. D., Parsons, D. W., Jones, S., Lin, J., Sjöblom, T., Leary, R. J., Shen, D., Boca, S. M., Barber, T., Ptak, J., et al. (2007) · Science · doi:10.1126/science.1145720 · Cited by 2,833 · see citing works
Protein Structure Prediction and Structural Genomics
Baker, D., & Sali, A. (2001) · Science · doi:10.1126/science.1065659 · Cited by 1,587 · see citing works
Self-citationA global genetic interaction network maps a wiring diagram of cellular function
Costanzo, M., VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., et al. (2016) · Science · doi:10.1126/science.aaf1420 · Cited by 1,240 · see citing works
Structure-based prediction of protein–protein interactions on a genome-wide scale
Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. (2012) · Nature · doi:10.1038/nature11503 · Cited by 723 · see citing works
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730 · see citing works
“Fortunately, the active and binding sites are frequently more conserved than the rest of the fold, and are thus modeled more accurately (Sanchez and Sali, 1998).”
BackgroundA systematic study of low-resolution recognition in protein-protein complexes
Vakser, I. A., Matar, O. G., & Lam, C. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.15.8477 · Cited by 180 · see citing works
Pandini, A., Denison, M. S., Song, Y., Soshilov, A. A., & Bonati, L. (2007) · Biochemistry · doi:10.1021/bi061460t · Cited by 160 · see citing works
Romanowski, M. J., Soccio, R. E., Breslow, J. L., & Burley, S. K. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052140699 · Cited by 162 · see citing works
- Authors
- Sánchez, R., & Sali, A.
- Affiliations
- Rockefeller University (US)
- Laboratories of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021
- ORCID
- Sánchez, Roberto
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1998-11-10
- Volume
- 95
- Issue
- 23
- Pages
- 13597-13602
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC24864
- OpenAlex
- W1972436355
- Cited by
- 362
- References
- 1
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 1 · 2023: 3 · 2021: 7 · 2020: 5 · 2019: 6 · 2018: 2 · 2017: 5 · 2016: 8 · 2015: 8 · 2014: 8 · 2013: 13 · 2012: 8
- FWCI
- 11.07
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM54762, R29GM054762, R01GM054762)
- 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 › Genomics and Phylogenetic Studies
- Keywords
- protein structure prediction, comparative protein structure modeling, Saccharomyces cerevisiae, yeast proteins, model evaluation
- MeSH terms
- Fungal Proteins, Models, Molecular, Protein Conformation, Saccharomyces cerevisiae, Genome, Fungal
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