Evidence map›Paper›PMID 28864946›Full record

ArticleJournal of computer-aided molecular design2017

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers.

Han Cao, Marcus C K Ng, Siti Azma Jusoh, Hio Kuan Tai, Shirley W I Siu

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In one paragraph

Article in Journal of computer-aided molecular design, 2017. 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
0.4field-weighted citation impact, top 36% 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

3 citing papers in PubMed, 6 citations in OpenAlex.

  1. A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain.International journal of molecular sciences · 2022
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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

5 authors at 2 institutions in 2 countries.

Han CaoDepartment of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida da Universidade, Taipa, Macau, China.
Marcus C K NgDepartment of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida da Universidade, Taipa, Macau, China.
Siti Azma JusohDepartment of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, 42300 Bandar Puncak Alam, Selangor, Malaysia.
Hio Kuan TaiDepartment of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida da Universidade, Taipa, Macau, China.
Shirley W I SiuDepartment of Computer and Information Science, Faculty of Science and Technology, University of Macau, Avenida da Universidade, Taipa, Macau, China. shirleysiu@umac.mo.
University of Macau · MOUniversiti Teknologi MARA · MY

Funding

Universidade de Macau MYRG2014-00104-FST
6 · The paper itself

Abstract

[Formula: see text]-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577-585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM . Website is implemented in PHP, MySQL and Apache, with all major browsers supported.

Indexed as

AlgorithmsModels, MolecularDrug DesignHumansMembrane ProteinsMolecular ConformationProtein DomainsProtein MultimerizationProtein Structure, SecondaryQuantitative Structure-Activity RelationshipMembrane ProteinsBioinformaticsBitopic dimerHelix assemblyHelix packingScwrl4Structure prediction

Identifiers

PMID28864946
OpenAlexW2751050863

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.