The DOI matches its Crossref record.
Free energy calculations: Applications to chemical and biochemical phenomena
Abstract
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFree energy calculations: Applications to chemical and biochemical phenomenaPeter. KollmanCite this: Chem. Rev. 1993, 93, 7, 2395–2417Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/cr00023a004https://doi.org/10.1021/cr00023a004research-articleACS PublicationsRequest reuse permissionsArticle Views7183Altmetric-Citations1769LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
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
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-citationMolecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
Wang, L., Wu, Y., Deng, Y., Kim, B., Pierce, L., Krilov, G., Lupyan, D., Robinson, S., Dahlgren, M. K., Greenwood, J., et al. (2015) · Journal of the American Chemical Society · doi:10.1021/ja512751q · Cited by 1,313
Massova, I., & Kollman, P. A. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008763014207 · Cited by 1,015
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
Calculation of absolute protein–ligand binding free energy from computer simulations
Woo, H.-J., & Roux, B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409005102 · Cited by 661
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
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct3008099 · Cited by 343
Using AMBER18 for Relative Free Energy Calculations
Song, L. F., Lee, T.-S., Zhu, C., York, D. M., & Merz, K. M. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00105 · Cited by 234
Rocklin, G. J., Mobley, D. L., Dill, K. A., & Hünenberger, P. H. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4826261 · Cited by 234
A gate in the selectivity filter of potassium channels
Bernèche, S., & Roux, B. (2005) · Structure · doi:10.1016/j.str.2004.12.019 · Cited by 214
Cui, Q., Sulea, T., Schrag, J. D., Munger, C., Hung, M.-N., Naïm, M., Cygler, M., & Purisima, E. O. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.04.035 · Cited by 162
Computational studies of membrane channels
Roux, B., & Schulten, K. (2004) · Structure · doi:10.1016/j.str.2004.06.013 · Cited by 145
Exploration, Sampling, And Reconstruction of Free Energy Surfaces with Gaussian Process Regression
Mones, L., Bernstein, N., & Csányi, G. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.6b00553 · Cited by 91
Fragment Informatics and Computational Fragment‐Based Drug Design: An Overview and Update
Sheng, C., & Zhang, W. (2013) · Medicinal Research Reviews · doi:10.1002/med.21255 · Cited by 80
New Coarse Variables for the Accurate Determination of Standard Binding Free Energies
Fu, H., Cai, W., Hénin, J., Roux, B., & Chipot, C. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00791 · Cited by 74
Jämbeck, J. P. M., & Lyubartsev, A. P. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp4111234 · Cited by 73
Dourado, D. F. A. R., & Flores, S. C. (2014) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.24634 · Cited by 56
Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome
Allnér, O., & Nilsson, L. (2011) · RNA · doi:10.1261/rna.029231.111 · Cited by 50
Free energy perturbation calculations of the thermodynamics of protein side-chain mutations
Steinbrecher, T., Abel, R., Clark, A., & Friesner, R. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.03.002 · Cited by 46
Peck Justice, S. A., Barron, M. P., Qi, G. D., Wijeratne, H. R. S., Victorino, J. F., Simpson, E. R., Vilseck, J. Z., Wijeratne, A. B., & Mosley, A. L. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.014576 · Cited by 28
Peck Justice, S. A., Qi, G., Wijeratne, H. R. S., Victorino, J. F., Simpson, E. R., Wijeratne, A. B., & Mosley, A. L. (2019) · doi:10.1101/2019.12.30.891267 · Cited by 28
Wei, D., Zheng, H., Su, N., Deng, M., & Lai, L. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci900463u · Cited by 22
Scoring Functions for Protein–Ligand Interactions
Sotriffer, C. (2012) · Protein‐Ligand Interactions · doi:10.1002/9783527645947.ch12 · Cited by 16
FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning
de Oliveira, C., Leswing, K., Feng, S., Kanters, R., Abel, R., & Bhat, S. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00681 · Cited by 15
Metadata
- Authors
- Kollman, P.
- Venue
- Chemical Reviews
- Publisher
- American Chemical Society (ACS)
- Published
- 1993-11-01
- Volume
- 93
- Issue
- 7
- Pages
- 2395-2417
- ISSN
- 0009-2665 (ISSN-L)
- 1520-6890
- OpenAlex
- W2043429268
- Cited by
- 2,101
- References
- 0
- FWCI
- 22.34
- 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
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.