Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.

Antonina Andreeva

Open access · hybridAbstract readReview

In one paragraph

Review in Biochemical Society transactions, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it

0cells of the map it votes in

2citing papers in PubMed

0.5field-weighted citation impact, top 29% 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

2 citing papers in PubMed, 4 citations in OpenAlex.

Functional Site Discovery From Incomplete Training Data: A Case Study With Nucleic Acid-Binding Proteins.Frontiers in genetics · 2019
Article
Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms.PloS one · 2017
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

1 author at 1 institution in 1 country.

Antonina AndreevaMRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K. tony@mrc-lmb.cam.ac.uk.

MRC Laboratory of Molecular Biology · GB

Funding

Medical Research Council G0100305Medical Research Council MC_U105185859Medical Research Council MC_U105192716

6 · The paper itself

Abstract

The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the ability to fold into alternative structures. This article reviews cases of structural variations observed for individual proteins and among groups of homologues, knowledge of which is essential for protein structure modelling.

Indexed as

Models, MolecularProtein ConformationAlgorithmsComputer SimulationProteinsProteinshomology modellingmetamorphic proteinsprotein structure evolutionStructural Classification of Proteins (SCOP)

Identifiers

PMID27284063

DOI10.1042/BST20160053

PMCPMC5011417

OpenAlexW2418297233

What OpenQuestion holds

Textmetadata

LicenceCC BY

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.