Sequence Similarity Searching

Hu, Gang; Kurgan, Lukasz

doi:10.1002/cpps.71

Cited by 57 publications

(37 citation statements)

References 52 publications

(53 reference statements)

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“…Findings of this data are in line with published data, in which PSI-BLAST was applied to study sequence similarity in protein (Altschul et al 1997), (Aravind and Koonin 1999) (Hu and Kurgan 2019).…”

Section: Figure 1 List Of Top Fifteen Homologous Proteins Retrieved Asupporting

confidence: 90%

“…These interacted residues have a different role in the organism: alanine is involved in the sugar metabolism and its deficiency is seen in cases like hypoglycemia, elevated insulin and glucagon levels (Shi et al 2002) Glutamine is involved in maintaining normal and steady blood sugar levels (Burke et al 1989). Docking approach has been proven to give insights with regards to explain protein-protein interaction or protein-ligand interaction, at molecular level; published data (Du et al 2016), (Burke et al 1989), (Hu and Kurgan 2019) are in accordance with findings of this research.…”

Section: Figuresupporting

confidence: 84%

“…These results suggest that the predicted model was of high quality (Figure-6) as similar data were published by researchers who used ERRAT and PROCHECK to investigate the quality of predicted models (Altschul et al 1997), (Aravind and Koonin 1999) (Hu and Kurgan 2019).…”

Section: 2three Dimension Structure Model Predictionsupporting

confidence: 80%

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In Silico Studies on Structural Function of Melanin Concentrating Hormone Receptor 1 Through Docking Approach, Towards Designing Drug for Treating Obesity

Mutangana¹,

Narcisse²,

Gaetan³

et al. 2020

RJESTE

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Melanin concentrating hormone receptor 1 is a G-protein coupled protein receptor expressed in the lateral hypothalamus and zona incerta, part of the nervous system that regulates feeding behavior and energy homeostasis. It is involved in the stimulation of appetite, this was seen when synthetic MCHR1 or MCH was administered to mice and it resulted in induced obesity due to the enhanced feeding. Many researchers have successfully find out the functions of several proteins, using computational approach. It is in this context that in this study the structural function of melanin concentrating hormone receptor 1 through docking studies has been done to make sure that those who are working to address the problem of obesity while trying to discover the effective drugs gain much insight about this receptor. The in silico methods have been used to predict the model of melanin concentrating hormone receptor 1. The template used for model prediction was human delta opioid receptor with the accession number 4N6H. The predicted model has been evaluated and found to be of good quality. Docking was done to investigate the interaction between the ligand; a bifunctional peptide ‘1-oleoyl-r-glycerol’ and the predicted model of melanin concentrating hormone receptor 1 which showed that fourteen residues interacted between the predicted model and ligand. Among interacting residues, it was realized that some of them are involved in sugar metabolism. Thus this study suggests a potential candidate for drug design against cancer and diabetes. Keywords: obesity, MCHR-1, docking, structural function, 3D structure, phylogenetic analysis, interacting residues

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Section: Figure 1 List Of Top Fifteen Homologous Proteins Retrieved Asupporting

confidence: 90%

Section: Figuresupporting

confidence: 84%

See 1 more Smart Citation

In Silico Studies on Structural Function of Melanin Concentrating Hormone Receptor 1 Through Docking Approach, Towards Designing Drug for Treating Obesity

Mutangana¹,

Narcisse²,

Gaetan³

et al. 2020

RJESTE

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“…To do that, we first created a dataset of the PDB sequences that were structured by masking residues in these sequences that lacked structure. We aligned segments of the DisProt sequences that lack annotations into these masked PDB sequences with Basic Local Alignment Search Tool (BLAST) [116,117]. We annotated the DisProt segments that shared ≥90% similarity and had an e-value ≤0.1 with at least one masked PDB sequence as structured.…”

Section: Benchmark Datasetmentioning

confidence: 99%

Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins

Katuwawala

Kurgan

2020

Biomolecules

Self Cite

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With over 60 disorder predictors, users need help navigating the predictor selection task. We review 28 surveys of disorder predictors, showing that only 11 include assessment of predictive performance. We identify and address a few drawbacks of these past surveys. To this end, we release a novel benchmark dataset with reduced similarity to the training sets of the considered predictors. We use this dataset to perform a first-of-its-kind comparative analysis that targets two large functional families of disordered proteins that interact with proteins and with nucleic acids. We show that limiting sequence similarity between the benchmark and the training datasets has a substantial impact on predictive performance. We also demonstrate that predictive quality is sensitive to the use of the well-annotated order and inclusion of the fully structured proteins in the benchmark datasets, both of which should be considered in future assessments. We identify three predictors that provide favorable results using the new benchmark set. While we find that VSL2B offers the most accurate and robust results overall, ESpritz-DisProt and SPOT-Disorder perform particularly well for disordered proteins. Moreover, we find that predictions for the disordered protein-binding proteins suffer low predictive quality compared to generic disordered proteins and the disordered nucleic acids-binding proteins. This can be explained by the high disorder content of the disordered protein-binding proteins, which makes it difficult for the current methods to accurately identify ordered regions in these proteins. This finding motivates the development of a new generation of methods that would target these difficult-to-predict disordered proteins. We also discuss resources that support users in collecting and identifying high-quality disorder predictions.

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“…GenBank (Benson et al, 2018) were used as a reference library to identify the barcode sequences created in the present study. The comparison of COI sequences in BOLD was facilitated through 'identification engine' tool (http://www.boldsystems.org/index.php/IDS_OpenIdEngine) and in GenBank through Basic Local Alignment Searching Tool (BLAST) (Altschul et al, 1990) using a standard similarity search protocol (Hu and Kurgan, 2018). Molecular Evolutionary Genetic analysis (MEGA) version X (Kumar et al, 2018) was used for neighbour-joining (NJ) tree construction using Kimura 2 parameters (K2P).…”

Section: Dna Sequence Analysismentioning

confidence: 99%

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

PrasannaKumar

Manikantan

Vijaylaxmi

et al. 2020

Preprint

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Environmental DNA (eDNA) barcoding technology is finding innovative applications in monitoring terrestrial and marine biodiversity. DNA barcode reference libraries containing barcodes for wide range of species is vital for the success of monitoring any environments using eDNA barcodes. Since amphipods are used as bio-indicators for monitoring environmental quality and its health, we used DNA barcodes of amphipods to test the efficacy of present DNA libraries for species identification. We barcoded 22 amphipod species belonging to 17 genera of 13 families. 50% of barcodes produced in the present study was generated for the first time, as the sequences were absent in GenBank and Barcode of Life Databases (BOLD). Tree based identification method used in the present study precisely clustered the generated sequences with reference sequences. Besides exploring the distribution of recorded amphipod species, we show that with advent of next generation sequencing technologies, reference datasets such as ours will become essential for assessing health and monitoring various environments using amphipod barcodes.

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Sequence Similarity Searching

Cited by 57 publications

References 52 publications

In Silico Studies on Structural Function of Melanin Concentrating Hormone Receptor 1 Through Docking Approach, Towards Designing Drug for Treating Obesity

In Silico Studies on Structural Function of Melanin Concentrating Hormone Receptor 1 Through Docking Approach, Towards Designing Drug for Treating Obesity

Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

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