The DOI matches its Crossref record.
Free Energy Simulations Come of Age: Protein−Ligand Recognition
Abstract
In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide an understanding of the interactions involved that goes beyond, and is an important complement to, experimental studies. Poisson-Boltzmann electrostatic models provide a faster and simpler free energy method in cases where electrostatic interactions are important. We illustrate both molecular dynamics and Poisson-Boltzmann methods with a detailed study of amino acid recognition by aspartyl-tRNA synthetase, whose specificity is important for maintaining the integrity of the genetic code.
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
Cited by
Molecular dynamics simulations of biomolecules
Karplus, M., & McCammon, J. A. (2002) · Nature Structural Biology · doi:10.1038/nsb0902-646 · Cited by 3,386
Self-citationHot spots—A review of the protein–protein interface determinant amino‐acid residues
Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21396 · Cited by 760
Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm060522a · Cited by 699
Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
Boresch, S., Tettinger, F., Leitgeb, M., & Karplus, M. (2003) · The Journal of Physical Chemistry B · doi:10.1021/jp0217839 · Cited by 569
Self-citationBrunk, E., & Rothlisberger, U. (2015) · Chemical Reviews · doi:10.1021/cr500628b · Cited by 494
Metadata
- Authors
- Simonson, T., Archontis, G., & Karplus, M.
- Venue
- Accounts of Chemical Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-03-27
- Volume
- 35
- Issue
- 6
- Pages
- 430-437
- ISSN
- 0001-4842 (ISSN-L)
- 1520-4898
- OpenAlex
- W2022879191
- Cited by
- 378
- References
- 0
- FWCI
- 5.94
- 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: Free Energy Simulations Come of Age: Protein−Ligand Recognition. https://app.cochat.ai/papers/10.1021/ar010030m
- The paper
- Simonson, T., Archontis, G., & Karplus, M. (2002). Free Energy Simulations Come of Age: Protein−Ligand Recognition. Accounts of Chemical Research. https://doi.org/10.1021/ar010030m
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.
