AMASS: a database for investigating protein structures.

Clinton J Mielke, Lawrence J Mandarino, Valentin Dinu

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it

0cells of the map it votes in

3citing 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

3 citing papers in PubMed.

Fuel Selection in Skeletal Muscle Exercising at Low Intensity; Reliance on Carbohydrate in Very Sedentary Individuals.Metabolic syndrome and related disorders · 2023
Article
PJAMIA open · 2021
Article
Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access.Proteomics · 2015
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.

Clinton J MielkeBiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USABiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USABiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

Lawrence J MandarinoBiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

Valentin DinuBiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

Funding

MOLECULAR REGULATION OF MUSCLE GLUCOSE METABOLISM IN MANR01DK047936 · NIDDK · UNIVERSITY OF TEXAS HLTH SCI CTR SAN ANT · PI MANDARINO, LAWRENCE J · 1994 to 2022

$10.7M

NIDDK NIH HHS R01DK04793NIDDK NIH HHS R01 DK047936

6 · The paper itself

Abstract

motivationModern techniques have produced many sequence annotation databases and protein structure portals, but these Web resources are rarely integrated in ways that permit straightforward exploration of protein functional residues and their co-localization.

resultsWe have created the AMASS database, which maps 1D sequence annotation databases to 3D protein structures with an intuitive visualization interface. Our platform also provides an analysis service that screens mass spectrometry sequence data for post-translational modifications that reside in functionally relevant locations within protein structures. The system is built on the premise that functional residues such as active sites, cancer mutations and post-translational modifications within proteins may co-localize and share common functions. AVAILABILITY AND IMPLEMENTATION: AMASS database is implemented with Biopython and Apache as a freely available Web server at amass-db.org.

Indexed as

Databases, ProteinProtein ConformationHumansInternetMass SpectrometryMitochondrial Proton-Translocating ATPasesMolecular Sequence AnnotationProtein Processing, Post-TranslationalProteinsPyruvate Dehydrogenase ComplexSequence Analysis, ProteinATP5F1B protein, humanMitochondrial Proton-Translocating ATPasesProteinsPyruvate Dehydrogenase Complex

Identifiers

PMID24497503

DOI10.1093/bioinformatics/btu073

PMCPMC4029036

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.