Computational Approach for Protein Structure Prediction

Venkatesan, Amouda; Gopal, Jeyakodi; Candavelou, Manimozhi; Gollapalli, Sowjanya; Karthikeyan, K

doi:10.4258/hir.2013.19.2.137

Cited by 15 publications

(5 citation statements)

References 15 publications

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“…The chimeric EiCh tertiary structure was modelled using ab initio approach, and the model was of good quality based on analysis using a Ramachandran plot and Z‐score. It has been reported that ab initio template‐free modelling is superior to other modelling methods (Venkatesan et al., 2013).…”

Section: Discussionmentioning

confidence: 99%

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Machimbirike

Pornputtapong

Senapin

et al. 2021

Journal of Fish Diseases

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Edwardsiella ictaluri infects several fish species and protection of the all the susceptible fish hosts from the pathogen using a monovalent vaccine is impossible because the species is composed of host-based genotypes that are genetic, serological and antigenic heterogenous. Here, immunoinformatic approach was employed to design a cross-immunogenic chimeric EiCh protein containing multi-epitopes. The chimeric EiCh protein is composed of 11 B-cell epitopes and 7 major histocompatibility complex class II epitopes identified from E. ictaluri immunogenic proteins previously reported.The 49.32 kDa recombinant EiCh protein was expressed in vitro in Escherichia coli BL-21 (DE3) after which inclusion bodies were successfully solubilized and refolded.Ab initio protein modelling revealed secondary and tertiary structures. Secondary structure was confirmed by circular dichroism spectroscopy. Antigenicity of the chimeric EiCh protein was exhibited by strong reactivity with serum from striped catfish and Nile tilapia experimentally infected with E. ictaluri. Furthermore, immunogenicity of the chimeric EiCh protein was investigated in vivo in Nile tilapia juveniles and it was found that the protein could strongly induce production of specific antibodies conferring agglutination activity and partially protected Nile tilapia juveniles with a relative survival percentage (RPS) of 42%. This study explored immunoinformatics as reverse vaccinology approach in vaccine design for aquaculture to manage E. ictaluri infections.

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Section: Discussionmentioning

confidence: 99%

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Machimbirike

Pornputtapong

Senapin

et al. 2021

Journal of Fish Diseases

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“…Computational protein structure prediction is highly beneficial in gaining insights on the protein function and drugs screening. [9]…”

Section: Methodsmentioning

confidence: 99%

Virtual screening of a MDR-TB WhiB6 target identified by gene expression profiling

2019

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Multidrug resistance in M. tb has become a huge global problem due to drug resistance. Hence, the treatment remains a challenge, even though short term chemotherapy is available. Therefore, it is of interest to identify novel drug targets in M.tb through gene expression profiling complimented by a subtractive proteome model. WhiB6 is a transcriptional regulator protein and a known drug resistant marker that is critical in the secretion dependent regulation of ESX-1, which is specialized for the deployment of host membrane-targeting proteins. The WhiB6 protein structure was modelled ab initio and was docked with a library of 173 phytochemicals with potential antituberculosis activity to the identified drug marker to find novel lead molecules. UDP-galactopyranose and GDP-L-galactose were identified to be potential lead molecules to inhibit the target WhiB6. The results were compared with the first line drugs for MDR-TB by docking with WhiB6. Data showed that Ethambutol showed better binding ability to WhiB6 but the afore mentioned top ranked phytochemicals were found to be better candidate molecules. The chosen candidate lead molecules should be further validated by suitable in vitro or in vivo investigation. Background: Every year about 10 million people are affected by tuberculosis and among which 1.6 million people die. [1-2] Across the world about 10 million people developed tuberculosis as of 2017 about two third of all new cases occurred in 8 countries like

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“…In [46] is proposed an algorithm that combines techniques of Self-Organization with Genetic Algorithm for PSP problem (SOGA-PSP). To automate the selection of parameter values (crossover and mutation rates), the influence of auto-adaptation is used to design genetic operators in order to optimize the protein prediction process.…”

Section: Genetic Algorithm Approachesmentioning

confidence: 99%

Ab Initio Protein Structure Prediction Using Evolutionary Approach: A Survey

Siqueira¹,

Venske²

2021

RITA

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Protein Structure Prediction (PSP) problem is to determine the three-dimensional structure of a protein only from its primary structure. Misfolding of a protein causes human diseases. Thus, the knowledge of the structure and functionality of proteins, combined with the prediction of their structure is a complex problem and a challenge for the area of computational biology. The metaheuristic optimization algorithms are naturally applicable to support in solving NP-hard problems.These algorithms are bio-inspired, since they were designed based on procedures found in nature, such as the successful evolutionary behavior of natural systems. In this paper, we present a survey on methods to approach the \textit{ab initio} protein structure prediction based on evolutionary computing algorithms, considering both single and multi-objective optimization. An overview of the works is presented, with some details about which characteristics of the problem are considered, as well as specific points of the algorithms used. A comparison between the approaches is presented and some directions of the research field are pointed out.

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Computational Approach for Protein Structure Prediction

Cited by 15 publications

References 15 publications

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

A multi‐epitope chimeric protein elicited a strong antibody response and partial protection against Edwardsiella ictaluri in Nile tilapia

Virtual screening of a MDR-TB WhiB6 target identified by gene expression profiling

Ab Initio Protein Structure Prediction Using Evolutionary Approach: A Survey

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