Evidence map›Paper›PMID 36959443›Full record

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

Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates.

Diego Javier Zea, Elin Teppa, Cristina Marino-Buslje

Abstract read
PubMed Publisher
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
2.5field-weighted citation impact, top 12% of its field
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

1 citing paper in PubMed, 3 citations in OpenAlex.

  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 at 2 institutions in 2 countries.

Diego Javier Zea *Laboratory of Computational and Quantitative Biology, LCQB, UMR 7238 CNRS, IBPS, Sorbonne Université, Paris, France.
Elin Teppa *Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
Cristina Marino-BusljeFundacion Instituto Leloir, Buenos Aires, Argentina. cmb@leloir.org.ar.
Centre National de la Recherche Scientifique · FRFundación Instituto Leloir · AR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Homology modeling is the most common technique to build structural models of a target protein based on the structure of proteins with high-sequence identity and available high-resolution structures. This technique is based on the idea that protein structure shows fewer changes than sequence through evolution. While in this scenario single mutations would minimally perturb the structure, experimental evidence shows otherwise: proteins with high conformational diversity impose a limit of the paradigm of comparative modeling as the same protein sequence can adopt dissimilar three-dimensional structures. These cases present challenges for modeling; at first glance, they may seem to be easy cases, but they have a complexity that is not evident at the sequence level. In this chapter, we address the following questions: Why should we care about conformational diversity? How to consider conformational diversity when doing template-based modeling in a practical way?

Indexed as

Molecular Dynamics SimulationProteinsAmino Acid SequenceProtein ConformationStructural Homology, ProteinProteinsComparative modelingConformational diversityConformational ensembleHomology modelingNative stateProtein dynamicsProtein structureStructural divergence

Identifiers

PMID36959443
OpenAlexW4360762439

What OpenQuestion holds

Textmetadata
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.