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Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl rin...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Manwi Shankar Majji Sai Sudha Rani Priyanka Gopi Arsha P Prateek Pandya Source Type: research

Revisiting structural organization of proteins at high temperature from a network perspective
Comput Biol Chem. 2023 Nov 3;108:107978. doi: 10.1016/j.compbiolchem.2023.107978. Online ahead of print.ABSTRACTInteractions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins ...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Suman Hait Sudip Kundu Source Type: research

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl rin...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Manwi Shankar Majji Sai Sudha Rani Priyanka Gopi Arsha P Prateek Pandya Source Type: research

Revisiting structural organization of proteins at high temperature from a network perspective
Comput Biol Chem. 2023 Nov 3;108:107978. doi: 10.1016/j.compbiolchem.2023.107978. Online ahead of print.ABSTRACTInteractions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins ...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Suman Hait Sudip Kundu Source Type: research

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl rin...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Manwi Shankar Majji Sai Sudha Rani Priyanka Gopi Arsha P Prateek Pandya Source Type: research

Revisiting structural organization of proteins at high temperature from a network perspective
Comput Biol Chem. 2023 Nov 3;108:107978. doi: 10.1016/j.compbiolchem.2023.107978. Online ahead of print.ABSTRACTInteractions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins ...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Suman Hait Sudip Kundu Source Type: research

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl rin...
Source: Computational Biology and Chemistry - November 13, 2023 Category: Bioinformatics Authors: Manwi Shankar Majji Sai Sudha Rani Priyanka Gopi Arsha P Prateek Pandya Source Type: research

Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment
Comput Biol Chem. 2023 Nov 2;108:107975. doi: 10.1016/j.compbiolchem.2023.107975. Online ahead of print.ABSTRACTMonoamine oxidases are the enzymes involved in the management of brain homeostasis through oxidative deamination of monoamines such as neurotransmitters, tyramine etc. The excessive production of monoamine oxidase-B specifically results in numerous neurodegenerative disorders like Alzheimer's and Parkinson's diseases. Inhibitors of monoamine oxidase-B are applied in the management of these disorders. Here in this article we have developed robust hybrid descriptor based QSAR models related to 123 monoamine oxidase...
Source: Computational Biology and Chemistry - November 11, 2023 Category: Bioinformatics Authors: None Bhawna Sunil Kumar Parvin Kumar Ashwani Kumar Source Type: research

Correlation intensity index-index of ideality of correlation: A hyphenated target function for furtherance of MAO-B inhibitory activity assessment
Comput Biol Chem. 2023 Nov 2;108:107975. doi: 10.1016/j.compbiolchem.2023.107975. Online ahead of print.ABSTRACTMonoamine oxidases are the enzymes involved in the management of brain homeostasis through oxidative deamination of monoamines such as neurotransmitters, tyramine etc. The excessive production of monoamine oxidase-B specifically results in numerous neurodegenerative disorders like Alzheimer's and Parkinson's diseases. Inhibitors of monoamine oxidase-B are applied in the management of these disorders. Here in this article we have developed robust hybrid descriptor based QSAR models related to 123 monoamine oxidase...
Source: Computational Biology and Chemistry - November 11, 2023 Category: Bioinformatics Authors: None Bhawna Sunil Kumar Parvin Kumar Ashwani Kumar Source Type: research

4mC-CGRU: Identification of N4-Methylcytosine (4mC) sites using convolution gated recurrent unit in Rosaceae genome
Comput Biol Chem. 2023 Oct 30;107:107974. doi: 10.1016/j.compbiolchem.2023.107974. Online ahead of print.ABSTRACTAn epigenetic modification is DNA N4-methylcytosine (4mC) that affects several biological functions without altering the DNA nucleotides, including DNA conformation, cell development, replication, stability, and DNA structural changes. To prevent restriction enzyme from damaging self-DNA, 4mC performs a critical role in restriction-modification functions. Existing studies mainly focused on finding hand-crafted features to identify 4mC locations, but these methods are inefficient due to high time consuming and hi...
Source: Computational Biology and Chemistry - November 9, 2023 Category: Bioinformatics Authors: Abida Sultana Sadia Jannat Mitu Md Naimul Pathan Mohammed Nasir Uddin Md Ashraf Uddin Sunil Aryal Source Type: research

4mC-CGRU: Identification of N4-Methylcytosine (4mC) sites using convolution gated recurrent unit in Rosaceae genome
Comput Biol Chem. 2023 Oct 30;107:107974. doi: 10.1016/j.compbiolchem.2023.107974. Online ahead of print.ABSTRACTAn epigenetic modification is DNA N4-methylcytosine (4mC) that affects several biological functions without altering the DNA nucleotides, including DNA conformation, cell development, replication, stability, and DNA structural changes. To prevent restriction enzyme from damaging self-DNA, 4mC performs a critical role in restriction-modification functions. Existing studies mainly focused on finding hand-crafted features to identify 4mC locations, but these methods are inefficient due to high time consuming and hi...
Source: Computational Biology and Chemistry - November 9, 2023 Category: Bioinformatics Authors: Abida Sultana Sadia Jannat Mitu Md Naimul Pathan Mohammed Nasir Uddin Md Ashraf Uddin Sunil Aryal Source Type: research

Optimizing fetal health prediction: Ensemble modeling with fusion of feature selection and extraction techniques for cardiotocography data
Comput Biol Chem. 2023 Oct 31;107:107973. doi: 10.1016/j.compbiolchem.2023.107973. Online ahead of print.ABSTRACTCardiotocography (CTG) captured the fetal heart rate and the timing of uterine contractions. Throughout pregnancy, CTG intelligent categorization is crucial for monitoring fetal health and preserving proper fetal growth and development. Since CTG provides information on the fetal heartbeat and uterus contractions, which helps determine if the fetus is pathologic or not, obstetricians frequently use it to evaluate a child's physical health during pregnancy. In the past, obstetricians have artificially analyzed CT...
Source: Computational Biology and Chemistry - November 5, 2023 Category: Bioinformatics Authors: Ramdas Kapila Sumalatha Saleti Source Type: research

Optimizing fetal health prediction: Ensemble modeling with fusion of feature selection and extraction techniques for cardiotocography data
Comput Biol Chem. 2023 Oct 31;107:107973. doi: 10.1016/j.compbiolchem.2023.107973. Online ahead of print.ABSTRACTCardiotocography (CTG) captured the fetal heart rate and the timing of uterine contractions. Throughout pregnancy, CTG intelligent categorization is crucial for monitoring fetal health and preserving proper fetal growth and development. Since CTG provides information on the fetal heartbeat and uterus contractions, which helps determine if the fetus is pathologic or not, obstetricians frequently use it to evaluate a child's physical health during pregnancy. In the past, obstetricians have artificially analyzed CT...
Source: Computational Biology and Chemistry - November 5, 2023 Category: Bioinformatics Authors: Ramdas Kapila Sumalatha Saleti Source Type: research

Optimizing fetal health prediction: Ensemble modeling with fusion of feature selection and extraction techniques for cardiotocography data
Comput Biol Chem. 2023 Oct 31;107:107973. doi: 10.1016/j.compbiolchem.2023.107973. Online ahead of print.ABSTRACTCardiotocography (CTG) captured the fetal heart rate and the timing of uterine contractions. Throughout pregnancy, CTG intelligent categorization is crucial for monitoring fetal health and preserving proper fetal growth and development. Since CTG provides information on the fetal heartbeat and uterus contractions, which helps determine if the fetus is pathologic or not, obstetricians frequently use it to evaluate a child's physical health during pregnancy. In the past, obstetricians have artificially analyzed CT...
Source: Computational Biology and Chemistry - November 5, 2023 Category: Bioinformatics Authors: Ramdas Kapila Sumalatha Saleti Source Type: research

Optimizing fetal health prediction: Ensemble modeling with fusion of feature selection and extraction techniques for cardiotocography data
Comput Biol Chem. 2023 Oct 31;107:107973. doi: 10.1016/j.compbiolchem.2023.107973. Online ahead of print.ABSTRACTCardiotocography (CTG) captured the fetal heart rate and the timing of uterine contractions. Throughout pregnancy, CTG intelligent categorization is crucial for monitoring fetal health and preserving proper fetal growth and development. Since CTG provides information on the fetal heartbeat and uterus contractions, which helps determine if the fetus is pathologic or not, obstetricians frequently use it to evaluate a child's physical health during pregnancy. In the past, obstetricians have artificially analyzed CT...
Source: Computational Biology and Chemistry - November 5, 2023 Category: Bioinformatics Authors: Ramdas Kapila Sumalatha Saleti Source Type: research