Evidence map›Paper›PMID 36959440›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling.

Damian Bartuzi, Agnieszka A Kaczor, Dariusz Matosiuk

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

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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

1 citing paper in PubMed.

  1. 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.

Damian BartuziDepartment of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland. damian.bartuzi@umlub.pl.
Agnieszka A KaczorDepartment of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland.
Dariusz MatosiukDepartment of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Homology modeling was long considered a method of choice in tertiary protein structure prediction. However, it used to provide models of acceptable quality only when templates with appreciable sequence identity with a target could be found. The threshold value was long assumed to be around 20-30%. Below this level, obtained sequence identity was getting dangerously close to values that can be obtained by chance, after aligning any random, unrelated sequences. In these cases, other approaches, including ab initio folding simulations or fragment assembly, were usually employed. The most recent editions of the CASP and CAMEO community-wide modeling methods assessment have brought some surprising outcomes, proving that much more clues can be inferred from protein sequence analyses than previously thought. In this chapter, we focus on recent advances in the field of difficult protein modeling, pushing the threshold deep into the "twilight zone", with particular attention devoted to improvements in applications of machine learning and model evaluation.

Indexed as

Machine LearningProteinsComputational BiologyDatabases, ProteinProtein ConformationProtein FoldingProtein Structure, TertiarySequence Analysis, ProteinProteinsAb initio modelingCAMEOCASPContact predictionDeep learningHomology modelingProtein foldingProtein structure prediction

Identifiers

PMID36959440

What OpenQuestion holds

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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.