Evidence map›Paper›PMID 30721054›Full record

ArticleJournal of chemical theory and computation2019

Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins.

María Del Carmen Marín, Luca De Vico, Sijia S Dong, Laura Gagliardi, Donald G Truhlar, Massimo Olivucci

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol.Topics in current chemistry (Cham) · 2022
    Review
  5. Review
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

6 authors.

María Del Carmen MarínDepartment of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy.ORCID http://orcid.org/0000-0001-6603-1692
Luca De VicoDepartment of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy.ORCID http://orcid.org/0000-0002-2821-5711
Sijia S DongDepartment of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States.ORCID http://orcid.org/0000-0001-8182-6522
Laura GagliardiDepartment of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States.ORCID http://orcid.org/0000-0001-5227-1396
Donald G TruhlarDepartment of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States.ORCID http://orcid.org/0000-0002-7742-7294
Massimo OlivucciDepartment of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy.ORCID http://orcid.org/0000-0002-8247-209X

Funding

Computational Design of Highly Fluorescent RhodopsinsR15GM126627 · NIGMS · BOWLING GREEN STATE UNIVERSITY · PI OLIVUCCI, MASSIMO · 2018 to 2018
$337k
NIGMS NIH HHS R15 GM126627
6 · The paper itself

Abstract

A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multiconfiguration perturbation theory calculations. In the present work we benchmark the more affordable multiconfiguration pair-density functional theory (MC-PDFT) method whose accuracy has been recently validated for retinal chromophores in the gas phase, indicating that MC-PDFT could potentially be used to analyze large (e.g., few hundreds) sets of rhodopsin proteins. Here, we test this theory for a set of rhodopsin QM/MM models whose experimental absorption maxima (λ

Indexed as

AnimalsBacteriaBacteriorhodopsinsDatabases, ProteinHumansModels, MolecularProtein ConformationQuantum TheoryRhodopsinThermodynamicsBacteriorhodopsinsRhodopsin

Identifiers

PMID30721054
PMCPMC7096677

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.