Dissecting the structural and functional impact of SNPs located in the spinal muscular atrophy associated gene SMN1 using in silico analysis

Gene Reports ◽  
2019 ◽  
Vol 15 ◽  
pp. 100388 ◽  
Author(s):  
Shafaat Hossain ◽  
Md Ismail Hosen
Keyword(s):  
Spinal Muscular Atrophy ◽  
In Silico ◽  
Muscular Atrophy ◽  
In Silico Analysis ◽  
Functional Impact ◽  
Silico Analysis

scholarly journals Identification of SNPs in rice GPAT genes and in silico analysis of their functional impact on GPAT proteins

2021 ◽  
Vol 49 (3) ◽  
pp. 12346
Author(s):  
Imran SAFDER ◽  
Gaoneng SHAO ◽  
Zhonghua SHENG ◽  
Peisong HU ◽  
Shaoqing TANG
Keyword(s):  
In Silico ◽  
Association Studies ◽  
Rice Genome ◽  
In Silico Analysis ◽  
Gene Families ◽  
Coding Region ◽  
Rice Varieties ◽  
Functional Impact ◽  
Functional Snps ◽  
Silico Analysis

SNPs are the most common nucleotide variations in the genome. Functional SNPs in the coding region, known as nonsynonymous SNPs (nsSNPs), change amino acid residues and affect protein function. Identifying functional SNPs is an uphill task as it is difficult to correlate between variation and phenotypes in association studies. Computational in silico analysis provides an opportunity to understand the SNPs functional impact to proteins and facilitate experimental approaches in understanding the relationship between the phenotype and genotype. Advancement in sequencing technologies contributed to sequencing thousands of genomes. As a result, many public databases have been designed incorporating this sequenced data to explore nucleotide variations. In this study, we explored functional SNPs in the rice GPAT family (as a model plant gene family), using 3000 Rice Genome Sequencing Project data. We identified 1056 SNPs, among hundred rice varieties in 26 GPAT genes, and filtered 98 nsSNPs. We further investigated the structural and functional impact of these nsSNPs using various computational tools and shortlisted 13 SNPs having high damaging effects on protein structure. We found that rice GPAT genes can be influenced by nsSNPs and they might have a major effect on regulation and function of GPAT genes. This information will be useful to understand the possible relationships between genetic mutation and phenotypic variation, and their functional implication on rice GPAT proteins. The study will also provide a computational pathway to identify SNPs in other rice gene families.

Association of single-nucleotide polymorphisms of the KEAP1 gene with the risk of various human diseases and its functional impact using in silico analysis

2018 ◽  
Vol 137 ◽  
pp. 205-218 ◽  
Author(s):  
Umapathy Dhamodharan ◽  
Balashanmugam Ponjayanthi ◽  
Dornadula Sireesh ◽  
Elango Bhakkiyalakshmi ◽  
Kunka Mohanram Ramkumar
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
In Silico ◽  
In Silico Analysis ◽  
Human Diseases ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Impact ◽  
Silico Analysis

A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

2020 ◽  
Vol 47 (6) ◽  
pp. 398-408
Author(s):  
Sonam Tulsyan ◽  
Showket Hussain ◽  
Balraj Mittal ◽  
Sundeep Singh Saluja ◽  
Pranay Tanwar ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gallbladder Carcinoma ◽  
In Silico ◽  
In Silico Analysis ◽  
Transcriptomic Profile ◽  
Silico Analysis

Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME

2020 ◽  
Vol 27 (38) ◽  
pp. 6523-6535 ◽  
Author(s):  
Antreas Afantitis ◽  
Andreas Tsoumanis ◽  
Georgia Melagraki
Keyword(s):  
Data Analysis ◽  
Virtual Screening ◽  
In Silico ◽  
Model Development ◽  
In Silico Analysis ◽  
Material Design ◽  
Efficient Solutions ◽  
Biological Data ◽  
Cost Efficient ◽  
Silico Analysis

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

In-Silico Analysis of Chromone Containing Sulfonamide Derivatives as Human Carbonic Anhydrase Inhibitors

2013 ◽  
Vol 9 (4) ◽  
pp. 608-616 ◽  
Author(s):  
Zaheer Ul-Haq ◽  
Saman Usmani ◽  
Uzma Mahmood ◽  
Mariya al-Rashida ◽  
Ghulam Abbas
Keyword(s):  
Carbonic Anhydrase ◽  
In Silico ◽  
In Silico Analysis ◽  
Carbonic Anhydrase Inhibitors ◽  
Human Carbonic Anhydrase ◽  
Silico Analysis

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

Sign in / Sign up

Export Citation Format

Share Document