Evidence map›Paper›PMID 37365370›Full record

ArticleJournal of computer-aided molecular design2023

COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge.

Michael Diedenhofen, Frank Eckert, Selman Terzi

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In one paragraph

Article in Journal of computer-aided molecular design, 2023. 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. Article
  4. Predicting pRSC advances · 2025
    Article
  5. 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

3 authors.

Michael DiedenhofenDassault Systèmes Deutschland GmbH, Am Kabellager 11-13, 51063, Cologne, Germany. Michael.diedenhofen@3ds.com.ORCID 0000-0002-5724-1994
Frank EckertDassault Systèmes Deutschland GmbH, Am Kabellager 11-13, 51063, Cologne, Germany.ORCID 0000-0003-0986-6428
Selman TerziDassault Systèmes Deutschland GmbH, Am Kabellager 11-13, 51063, Cologne, Germany.

Funding

Advancing predictive physical modeling through focused development of model systems to drive new modeling innovationsR01GM124270 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI MOBLEY, DAVID LOWELL · 2018 to 2021
$1.5M
NIGMS NIH HHS R01 GM124270
6 · The paper itself

Abstract

The SAMPL8 blind prediction challenge, which addresses the acid/base dissociation constants (pKa) and the distribution coefficients (logD), was addressed by the Conductor like Screening Model for Realistic Solvation (COSMO-RS). Using the COSMOtherm implementation of COSMO-RS together with a rigorous conformational sampling, yielded logD predictions with a root mean square deviation (RMSD) of 1.36 log units over all 11 compounds and seven bi-phasic systems of the data set, which was the most accurate of all contest submissions (logD).For the SAMPL8 pKa competition, participants were asked to report the standard state free energies of all microstates, which were then used to calculate the macroscopic pKa. We have used COSMO-RS based linear free energy fit models to calculate the requested energies. The assignment of the calculated and experimental pKa values was made on the basis of the popular transitions, i.e. the transition hat was predicted by the majority of the submissions. With this assignment and a model that covers both, pKa and base pKa, we achieved an RMSD of 3.44 log units (18 pKa values of 14 molecules), which is the second place of the six ranked submissions. By changing to an assignment that is based on the experimental transition curves, the RMSD reduces to 1.65. In addition to the ranked contribution, we submitted two more data sets, one for the standard pKa model and one or the standard base pKa model of COSMOtherm. Using the experiment based assignment with the predictions of the two sets we received a RMSD of 1.42 log units (25 pKa values of 20 molecules). The deviation mainly arises from a single outlier compound, the omission of which leads to an RMSD of 0.89 log units.

Indexed as

WaterHumansMolecular ConformationThermodynamicsWaterCOSMO-RSCOSMOthermlogD predictionPartitioningpKa prediction

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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.