Evidence map›Paper›PMID 23861790›Full record

ArticlePloS one2013

Point charges optimally placed to represent the multipole expansion of charge distributions.

Ramu Anandakrishnan, Charles Baker, Saeed Izadi, Alexey V Onufriev

Abstract read
In one paragraph

Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed.

  1. Effects of glycans and hinge on dynamics in the IgG1 Fc.Journal of biomolecular structure & dynamics · 2024
    Article
  2. New experimental evidence for pervasive dynamics in proteins.Protein science : a publication of the Protein Society · 2023
    Article
  3. Fast Polarizable Water Model for Atomistic Simulations.Journal of chemical theory and computation · 2022
    Article
  4. Article
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  6. Review
  7. Prediction of experimental properties of COJournal of molecular modeling · 2019
    Article
  8. Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.Journal of chemical theory and computation · 2019
    Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Physics-based all-atom modeling of RNA energetics and structure.Wiley interdisciplinary reviews. RNA · 2017
    Review
  14. Article
  15. Accuracy limit of rigid 3-point water models.The Journal of chemical physics · 2016
    Article
  16. Article
  17. Building Water Models: A Different Approach.The journal of physical chemistry letters · 2014
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Ramu AnandakrishnanDepartment of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America.
Charles Baker
Saeed Izadi
Alexey V Onufriev

Funding

Analytical Electrostatics: Methods and Biological Applications.R01GM076121 · NIGMS · VIRGINIA POLYTECHNIC INST AND ST UNIV · PI ONUFRIEV, ALEXEY VLAD · 2006 to 2014
$2.6M
NIGMS NIH HHS GM076121NIGMS NIH HHS R01 GM076121
6 · The paper itself

Abstract

We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge approximation (OPCA) retains many of the useful properties of point multipole expansion, including the same far-field asymptotic behavior of the approximate potential. A general framework for numerically computing OPCA, for any given number of approximating charges, is described. We then derive a 2-charge practical point charge approximation, PPCA, which approximates the 2-charge OPCA via closed form analytical expressions, and test the PPCA on a set of charge distributions relevant to biomolecular modeling. We measure the accuracy of the new approximations as the RMS error in the electrostatic potential relative to that produced by the original charge distribution, at a distance 2x the extent of the charge distribution--the mid-field. The error for the 2-charge PPCA is found to be on average 23% smaller than that of optimally placed point dipole approximation, and comparable to that of the point quadrupole approximation. The standard deviation in RMS error for the 2-charge PPCA is 53% lower than that of the optimal point dipole approximation, and comparable to that of the point quadrupole approximation. We also calculate the 3-charge OPCA for representing the gas phase quantum mechanical charge distribution of a water molecule. The electrostatic potential calculated by the 3-charge OPCA for water, in the mid-field (2.8 Å from the oxygen atom), is on average 33.3% more accurate than the potential due to the point multipole expansion up to the octupole order. Compared to a 3 point charge approximation in which the charges are placed on the atom centers, the 3-charge OPCA is seven times more accurate, by RMS error. The maximum error at the oxygen-Na distance (2.23 Å) is half that of the point multipole expansion up to the octupole order.

Indexed as

Models, MolecularArginineHydrogen-Ion ConcentrationModels, StatisticalStatic ElectricityWaterArginineWater

Identifiers

PMID23861790
PMCPMC3701554

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.