The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies
Abstract
Noncovalent interactions are important in many physiological processes of complexation which involve all components of the living cells. Here we report an approach to computationally study the interaction free energies in protein−protein complexes which allows from a single simulation an estimate of the individual contribution of each residue to the binding. We developed this new technique computational alanine scanning and applied it to study the interactions of the oncoprotein Mdm2 to the N -terminal stretch of tumor suppressor protein p53. Excellent agreement has been found between the calculated and experimental data. This residue mutation methodology could prove to be a useful general design tool for molecules nucleotides, peptides, lipids, or any other organic compound optimized for interactions or stability, since one can qualitatively estimate the free energy consequences of many mutations from a single molecular dynamics trajectory.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain
Kussie, P. H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A. J., & Pavletich, N. P. (1996) · Science · doi:10.1126/science.274.5289.948 · Cited by 2,206
Amplification of a gene encoding a p53-associated protein in human sarcomas
Oliner, J. D., Kinzler, K. W., Meltzer, P. S., George, D. L., & Vogelstein, B. (1992) · Nature · doi:10.1038/358080a0 · Cited by 1,949
p53-Dependent apoptosis suppresses tumor growth and progression in vivo
Symonds, H., Krall, L., Remington, L., Saenz-Robles, M., Lowe, S., Jacks, T., & Van Dyke, T. (1994) · Cell · doi:10.1016/0092-8674(94)90534-7 · Cited by 880
Wild-type p53 activates transcription in vitro
Farmer, G., Bargonetti, J., Zhu, H., Friedman, P., Prywes, R., & Prives, C. (1992) · Nature · doi:10.1038/358083a0 · Cited by 579
Cited by
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., et al. (2000) · Accounts of Chemical Research · doi:10.1021/ar000033j · Cited by 4,978
Self-citationMMPBSA.py: An Efficient Program for End-State Free Energy Calculations
Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300418h · Cited by 4,609
Massova, I., & Kollman, P. A. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008763014207 · Cited by 1,015
Self-citationA simple physical model for binding energy hot spots in protein–protein complexes
Kortemme, T., & Baker, D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202485799 · Cited by 804
Molecular Recognition and Docking Algorithms
Brooijmans, N., & Kuntz, I. D. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142532 · Cited by 788
Metadata
- Authors
- Massova, I., & Kollman, P. A.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 1999-08-31
- Volume
- 121
- Issue
- 36
- Pages
- 8133-8143
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W1998645872
- Cited by
- 780
- References
- 4
- FWCI
- 6.42
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies. https://app.cochat.ai/papers/10.1021/ja990935j
- The paper
- Massova, I., & Kollman, P. A. (1999). Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies. Journal of the American Chemical Society. https://doi.org/10.1021/ja990935j
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
