Evidence map›Paper›PMID 38647745›Full record

ArticleBioresources and bioprocessing2022

Atomevo: a web server combining protein modelling, docking, molecular dynamic simulation and MMPBSA analysis of Candida antarctica lipase B (CalB) fusion protein.

Jin-Heng Hao, Dun-Jin Zheng, Yu-Hao Ye, Jie-Ting Yu, Xin-Yao Li, Mei-Jie Xiong, Wen-Hao Jiang, Kang-Ping He, Pei-Yu Li, Yong-Si Lv and 4 more

Open access · diamondAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioresources and bioprocessing, 2022. 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
0.5field-weighted citation impact, top 39% 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, 8 citations in OpenAlex.

  1. Review
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

14 authors at 2 institutions in 1 country.

Jin-Heng Hao *Guangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Dun-Jin Zheng *Guangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Yu-Hao Ye *School of Food Science, South China Agricultural University, Guangzhou, 510642, China.
Jie-Ting YuGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Xin-Yao LiGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Mei-Jie XiongGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Wen-Hao JiangGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Kang-Ping HeGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Pei-Yu LiGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Yong-Si LvGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Wei-Ming GuGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Lin-Hao LaiGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Yi-Da WuGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China.
Shi-Lin CaoGuangdong Key Laboratory of Food Intelligent Manufacturing, School of Food Science and Technology, Foshan University, Foshan, 528000, China. seelam.shilin.cao@gmail.com.ORCID http://orcid.org/0000-0002-7702-5279
Foshan University · CNSouth China Agricultural University · CN

Funding

Guangdong Basic and Applied Basic Research Foundation 2019A1515110621The High-Level Talent Start-Up Research Project of Foshan University GG07016The Project of Department of Education of Guangdong Province 2017KQNCX217
6 · The paper itself

Abstract

Although current computational biology software is available and has prompted the development of enzyme-substrates simulation, they are difficult to install and inconvenient to use. This makes the time-consuming and error-prone process. By far there is still a lack of a complete tool which can provide a one-stop service for the enzyme-substrates simulation process. Hence, in this study, several computational biology software was extended development and integrated as a website toolbox named Atomevo. The Atomevo is a free web server providing a user-friendly interface for enzyme-substrates simulation: (1) protein homologous modeling; (2) parallel docking module of Autodock Vina 1.2; (3) automatic modeling builder for Gromacs molecular dynamics simulation package; and (4) Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis module for receptor-ligand binding affinity analysis. We officially launched the web server and provided instructions through a case for the design and simulation of Candida antarctica lipase B (CalB) fusion protein called Maltose Binding Protein-Thioredoxin A-Candida antarctica lipase B (MBP-TrxA-CalB).

Indexed as

BiofuelDockingMMPBSAMolecular dynamics simulationWeb Server

Identifiers

PMID38647745
PMCPMC10991163
OpenAlexW4280549151

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.