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THEMATICS: A simple computational predictor of enzyme function from structure
Open accessAbstract
We show that theoretical microscopic titration curves (THEMATICS) can be used to identify active-site residues in proteins of known structure. Results are featured for three enzymes: triosephosphate isomerase (TIM), aldose reductase (AR), and phosphomannose isomerase (PMI). We note that TIM and AR have similar structures but catalyze different kinds of reactions, whereas TIM and PMI have different structures but catalyze similar reactions. Analysis of the theoretical microscopic titration curves for all of the ionizable residues of these proteins shows that a small fraction (3–7%) of the curves possess a flat region where the residue is partially protonated over a wide pH range. The preponderance of residues with such perturbed curves occur in the active site. Additional results are given in summary form to show the success of the method for proteins with a variety of different chemistries and structures.
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Cited by
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Li, H., Robertson, A. D., & Jensen, J. H. (2005) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20660 · Cited by 2,054
Network Analysis of Protein Structures Identifies Functional Residues
Amitai, G., Shemesh, A., Sitbon, E., Shklar, M., Netanely, D., Venger, I., & Pietrokovski, S. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.10.055 · Cited by 499
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA
Rostkowski, M., Olsson, M. H., Søndergaard, C. R., & Jensen, J. H. (2011) · BMC Structural Biology · doi:10.1186/1472-6807-11-6 · Cited by 431
Automated protein function prediction--the genomic challenge
Friedberg, I. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbl004 · Cited by 366
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
Brylinski, M., & Skolnick, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707684105 · Cited by 333
Metadata
- Authors
- Ondrechen, M. J., Clifton, J. G., & Ringe, D.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2001-10-16
- Volume
- 98
- Issue
- 22
- Pages
- 12473-12478
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2045110975
- Cited by
- 226
- References
- 0
- FWCI
- 3.91
- Type
- journal article
- Language
- en
- Open access
- green
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- Ondrechen, M. J., Clifton, J. G., & Ringe, D. (2001). THEMATICS: A simple computational predictor of enzyme function from structure. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.211436698
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