Evidence map›Paper›PMID 33289893›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2021

Analysis of Protein Intermolecular Interactions with MAFFT-DASH.

John Rozewicki, Songling Li, Kazutaka Katoh, Daron M Standley

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2021. 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

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.

  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

4 authors.

John RozewickiResearch Institute for Microbial Diseases, Osaka University, Osaka, Japan.
Songling LiResearch Institute for Microbial Diseases, Osaka University, Osaka, Japan.
Kazutaka KatohResearch Institute for Microbial Diseases, Osaka University, Osaka, Japan.
Daron M StandleyResearch Institute for Microbial Diseases, Osaka University, Osaka, Japan. standley@biken.osaka-u.ac.jp.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Database of Aligned Structural Homologs (DASH) is a tool for efficiently navigating the Protein Data Bank (PDB) by means of pre-computed pairwise structural alignments. We recently showed that, by integrating DASH structural alignments with the multiple sequence alignment (MSA) software MAFFT, we were able to significantly improve MSA accuracy without dramatically increasing manual or computational complexity. In the latest DASH update, such queries are not limited to PDB entries but can also be launched from user-provided protein coordinates. Here, we describe a further extension of DASH that retrieves intermolecular interactions of all structurally similar domains in the PDB to a query domain of interest. We illustrate these new features using a model of the NYN domain of the ribonuclease N4BP1 as an example. We show that the protein-nucleotide interactions returned are distributed on the surface of the NYN domain in an asymmetric manner, roughly centered on the known nuclease active site.

Indexed as

SoftwareAlgorithmsAmino Acid SequenceComputational BiologyDatabases, ProteinNuclear ProteinsProtein BindingProtein DomainsRibonucleasesRNA-Binding ProteinsSequence AlignmentSequence Analysis, ProteinN4BP1 protein, humanNuclear ProteinsRibonucleasesRNA-Binding ProteinsBinding site predictionDatabase queryProtein-nucleotide interactionProtein-protein interactionProtein structural alignmentRibonucleaseRNA structureStructural domain

Identifiers

PMID33289893

What OpenQuestion holds

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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.