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Article ; Online: Evaluation of decursin and its isomer decursinol angelate as potential inhibitors of human glutamate dehydrogenase activity through in silico and enzymatic assay screening.

Chang, Sukkum Ngullie / Keretsu, Seketoulie / Kang, Sun Chul

2022 Volume 151, Issue Pt B, Page(s) 106287

Abstract: Glutaminolysis is a typical hallmark of malignant tumors across different cancers. Glutamate dehydrogenase (GDH, GLUD1) is one such enzyme involved in the conversion of glutamate to α-ketoglutarate. High levels of GDH are associated with numerous ... ...

Abstract	Glutaminolysis is a typical hallmark of malignant tumors across different cancers. Glutamate dehydrogenase (GDH, GLUD1) is one such enzyme involved in the conversion of glutamate to α-ketoglutarate. High levels of GDH are associated with numerous diseases and is also a prognostic marker for predicting metastasis in colorectal cancer. Therefore, inhibiting GDH can be a crucial therapeutic target. Here in this study, we performed molecular docking analysis of 8 different plants derived single compounds collected from pubChem database for screening and selected decursin (DN) and decursinol angelate (DA). We performed molecular dynamics simulation (MD), monitored the stability, interaction for protein and docked ligand at 50 ns, and evaluated the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation on the twoselected compounds along with a standard inhibitor epigallocatechin gallate (EGCG) as reference. The final results showed the formation of stable hydrogen bond interactions by DN and DA in the residues of R400 and Y386 at the ADP activation site of GDH, which was important for the selective inhibition of GDH activity. Additionally, the total binding energy of DN and DA were -115.5 kJ/mol and -106.2 kJ/mol, which was higher than the standard reference GDH inhibitor EGCG (-92.8 kJ/mol). Furthermore, biochemical analysis for GDH inhibition substantiated our computational results and established DN and DA as novel GDH inhibitor. The percentage of IC
Language	English
Publishing date	2022-11-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.106287
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Article ; Online: Molecular Modeling Studies of

Ghosh, Suparna / Keretsu, Seketoulie / Cho, Seung Joo

International journal of molecular sciences

2021 Volume 22, Issue 22

Abstract: Overexpression and frequent mutations in FMS-like tyrosine kinase-3 (FLT3) are considered risk factors for severe acute myeloid leukemia (AML). Hyperactive FLT3 induces premature activation of multiple intracellular signaling pathways, resulting in cell ... ...

Abstract	Overexpression and frequent mutations in FMS-like tyrosine kinase-3 (FLT3) are considered risk factors for severe acute myeloid leukemia (AML). Hyperactive FLT3 induces premature activation of multiple intracellular signaling pathways, resulting in cell proliferation and anti-apoptosis. We conducted the computational modeling studies of 40 pyrimidine-4,6-diamine-based compounds by integrating docking, molecular dynamics, and three-dimensional structure-activity relationship (3D-QSAR). Molecular docking showed that K644, C694, F691, E692, N701, D829, and F830 are critical residues for the binding of ligands at the hydrophobic active site. Molecular dynamics (MD), together with Molecular Mechanics Poison-Boltzmann/Generalized Born Surface Area, i.e., MM-PB(GB)SA, and linear interaction energy (LIE) estimation, provided critical information on the stability and binding affinity of the selected docked compounds. The MD study suggested that the mutation in the gatekeeper residue F691 exhibited a lower binding affinity to the ligand. Although, the mutation in D835 in the activation loop did not exhibit any significant change in the binding energy to the most active compound. We developed the ligand-based comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models. CoMFA (
MeSH term(s)	Amines/chemistry ; Amines/therapeutic use ; Binding Sites/drug effects ; Catalytic Domain/drug effects ; Computer Simulation ; Humans ; Leukemia, Myeloid, Acute/drug therapy ; Leukemia, Myeloid, Acute/genetics ; Leukemia, Myeloid, Acute/pathology ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/therapeutic use ; Pyrimidines/chemistry ; Pyrimidines/therapeutic use ; Quantitative Structure-Activity Relationship ; Signal Transduction/drug effects ; Structure-Activity Relationship ; fms-Like Tyrosine Kinase 3/antagonists & inhibitors ; fms-Like Tyrosine Kinase 3/chemistry ; fms-Like Tyrosine Kinase 3/genetics
Chemical Substances	Amines ; Ligands ; Protein Kinase Inhibitors ; Pyrimidines ; fms-Like Tyrosine Kinase 3 (EC 2.7.10.1) ; pyrimidine (K8CXK5Q32L)
Language	English
Publishing date	2021-11-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222212511
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Article: Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR.

Ghosh, Suparna / Keretsu, Seketoulie / Cho, Seung Joo

PeerJ

2021 Volume 9, Page(s) e11951

Abstract: Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth ... ...

Abstract	Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth muscle cell contraction in the vascular system. Inhibition of ROCK1 has been shown to be a promising therapy for patients with cardiovascular disease. In this study, we have conducted molecular modeling techniques such as docking, molecular dynamics (MD), and 3-Dimensional structure-activity relationship (3D-QSAR) on a series of N-ethyl-4-(pyridin-4-yl)benzamide-based compounds. Docking and MD showed critical interactions and binding affinities between ROCK1 and its inhibitors. To establish the structure-activity relationship (SAR) of the compounds, 3D-QSAR techniques such as Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were used. The CoMFA (
Language	English
Publishing date	2021-08-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.11951
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Article ; Online: Computer aided designing of novel pyrrolopyridine derivatives as JAK1 inhibitors.

Keretsu, Seketoulie / Ghosh, Suparna / Cho, Seung Joo

Scientific reports

2021 Volume 11, Issue 1, Page(s) 23051

Abstract: Janus kinases (JAKs) are a family of non-receptor kinases that play a key role in cytokine signaling and their aberrant activities are associated with the pathogenesis of various immune diseases. The JAK1 isoform plays an essential role in the types 1 ... ...

Abstract	Janus kinases (JAKs) are a family of non-receptor kinases that play a key role in cytokine signaling and their aberrant activities are associated with the pathogenesis of various immune diseases. The JAK1 isoform plays an essential role in the types 1 and II interferon signaling and elicits signals from the interleukin-2, interleukin-4, gp130, and class 2 receptor families. It is ubiquitously expressed in humans and its overexpression has been linked with autoimmune diseases such as myeloproliferative neoplasm. Although JAK1 inhibitors such as Tofacitinib have been approved for medical use, the low potency and off-target effects of these inhibitors have limited their use and calls for the development of novel JAK1 inhibitors. In this study, we used computational methods on a series of pyrrolopyridine derivatives to design new JAK1 inhibitors. Molecular docking and molecular dynamics simulation methods were used to study the protein-inhibitor interactions. 3D-quantitative structure-activity relationship models were developed and were used to predict the activity of newly designed compounds. Free energy calculation methods were used to study the binding affinity of the inhibitors with JAK1. Of the designed compounds, seventeen of the compounds showed a higher binding energy value than the most active compound in the dataset and at least six of the compounds showed higher binding energy value than the pan JAK inhibitor Tofacitinib. The findings made in this study could be utilized for the further development of JAK1 inhibitors.
MeSH term(s)	Chemistry, Pharmaceutical/methods ; Computational Biology ; Computer Simulation ; Drug Design ; Gene Expression Regulation, Neoplastic ; Humans ; Hydrogen Bonding ; Inhibitory Concentration 50 ; Janus Kinase 1/chemistry ; Janus Kinase Inhibitors ; Janus Kinases/metabolism ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Piperidines/pharmacology ; Protein Isoforms ; Protein Kinase Inhibitors/pharmacology ; Pyridines/chemistry ; Pyrimidines/pharmacology ; Quantitative Structure-Activity Relationship ; Software ; Static Electricity
Chemical Substances	Janus Kinase Inhibitors ; Ligands ; Piperidines ; Protein Isoforms ; Protein Kinase Inhibitors ; Pyridines ; Pyrimidines ; tofacitinib (87LA6FU830) ; JAK1 protein, human (EC 2.7.10.2) ; Janus Kinase 1 (EC 2.7.10.2) ; Janus Kinases (EC 2.7.10.2)
Language	English
Publishing date	2021-11-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-02364-2
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Article ; Online: Molecular Modelling Studies on Pyrazole Derivatives for the Design of Potent Rearranged during Transfection Kinase Inhibitors.

Bhujbal, Swapnil P / Keretsu, Seketoulie / Cho, Seung Joo

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 3

Abstract: RET (rearranged during transfection) kinase, one of the receptor tyrosine kinases, plays a crucial role in the development of the human nervous system. It is also involved in various cell signaling networks responsible for the normal cell division, ... ...

Abstract	RET (rearranged during transfection) kinase, one of the receptor tyrosine kinases, plays a crucial role in the development of the human nervous system. It is also involved in various cell signaling networks responsible for the normal cell division, growth, migration, and survival. Previously reported clinical studies revealed that deregulation or aberrant activation of RET signaling can cause several types of human cancer. For example, medullary thyroid carcinoma (MTC) and multiple endocrine neoplasia (MEN2A, MEN2B) occur due to sporadic mutation or germline RET mutation. A number of RET kinase inhibitors have been approved by the FDA for the treatment of cancer, such as cabozantinib, vandetanib, lenvatinib, and sorafenib. However, each of these drugs is a multikinase inhibitor. Hence, RET is an important therapeutic target for cancer drug design. In this work, we have performed various molecular modelling studies, such as molecular docking and dynamics simulation for the most active compound of the pyrazole series as RET kinase inhibitors. Furthermore, molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) free energy calculation and 3-dimensional quantitative structure-activity relationship (3D-QSAR) were performed using g_mmpbsa and SYBYL-X 2.1 package. The results of this study revealed the crucial binding site residues at the active site of RET kinase and contour map analysis showed important structural characteristics for the design of new highly active inhibitors. Therefore, we have designed ten RET kinase inhibitors, which showed higher inhibitory activity than the most active compound of the series. The results of our study provide insights to design more potent and selective RET kinase inhibitors.
MeSH term(s)	Antineoplastic Agents/pharmacology ; Carcinoma, Neuroendocrine/drug therapy ; Carcinoma, Neuroendocrine/metabolism ; Cell Line, Tumor ; Humans ; Molecular Docking Simulation/methods ; Protein Kinase Inhibitors/pharmacology ; Pyrazoles/pharmacology ; Quantitative Structure-Activity Relationship ; Receptor Protein-Tyrosine Kinases/metabolism ; Signal Transduction/drug effects ; Thyroid Neoplasms/drug therapy ; Thyroid Neoplasms/metabolism ; Transfection/methods
Chemical Substances	Antineoplastic Agents ; Protein Kinase Inhibitors ; Pyrazoles ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1)
Language	English
Publishing date	2021-01-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26030691
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Article ; Online: Molecular Modeling Study of c-KIT/PDGFRα Dual Inhibitors for the Treatment of Gastrointestinal Stromal Tumors.

Keretsu, Seketoulie / Ghosh, Suparna / Cho, Seung Joo

International journal of molecular sciences

2020 Volume 21, Issue 21

Abstract: Gastrointestinal stromal tumors (GISTs) are the most common Mesenchymal Neoplasm of the gastrointestinal tract. The tumorigenesis of GISTs has been associated with the gain-of-function mutation and abnormal activation of the stem cell factor receptor (c- ... ...

Abstract	Gastrointestinal stromal tumors (GISTs) are the most common Mesenchymal Neoplasm of the gastrointestinal tract. The tumorigenesis of GISTs has been associated with the gain-of-function mutation and abnormal activation of the stem cell factor receptor (c-KIT) and platelet-derived growth factor receptor alpha (PDGFRα) kinases. Hence, inhibitors that target c-KIT and PDGFRα could be a therapeutic option for the treatment of GISTs. The available approved c-KIT/PDGFRα inhibitors possessed low efficacy with off-target effects, which necessitated the development of potent inhibitors. We performed computational studies of 48 pyrazolopyridine derivatives that showed inhibitory activity against c-KIT and PDGFRα to study the structural properties important for inhibition of both the kinases. The derivative of phenylurea, which has high activities for both c-KIT (pIC
MeSH term(s)	Amino Acid Substitution ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/isolation & purification ; Antineoplastic Agents/pharmacokinetics ; Antineoplastic Agents/therapeutic use ; Binding Sites ; Drug Screening Assays, Antitumor/methods ; Gastrointestinal Neoplasms/drug therapy ; Gastrointestinal Stromal Tumors/drug therapy ; Humans ; Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutant Proteins/chemistry ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/isolation & purification ; Protein Kinase Inhibitors/pharmacokinetics ; Protein Kinase Inhibitors/therapeutic use ; Proto-Oncogene Proteins c-kit/antagonists & inhibitors ; Proto-Oncogene Proteins c-kit/chemistry ; Proto-Oncogene Proteins c-kit/genetics ; Proto-Oncogene Proteins c-kit/metabolism ; Pyrazoles/chemistry ; Pyridines/chemistry ; Quantitative Structure-Activity Relationship ; Receptor, Platelet-Derived Growth Factor alpha/antagonists & inhibitors ; Receptor, Platelet-Derived Growth Factor alpha/chemistry ; Receptor, Platelet-Derived Growth Factor alpha/genetics ; Receptor, Platelet-Derived Growth Factor alpha/metabolism
Chemical Substances	Antineoplastic Agents ; Mutant Proteins ; Protein Kinase Inhibitors ; Pyrazoles ; Pyridines ; pyrazolopyridine ; Proto-Oncogene Proteins c-kit (EC 2.7.10.1) ; Receptor, Platelet-Derived Growth Factor alpha (EC 2.7.10.1)
Language	English
Publishing date	2020-11-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21218232
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Article ; Online: Molecular modeling studies of pyrrolo[2,3-d]pyrimidin-4-amine derivatives as JAK1 inhibitors based on 3D-QSAR, molecular docking, molecular dynamics (MD) and MM-PBSA calculations.

Keretsu, Seketoulie / Bhujbal, Swapnil P / Cho, Seung Joo

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 3, Page(s) 753–765

Abstract: Rheumatoid Arthritis (RA) is an autoimmune disease caused by overproduction of pro-inflammatory cytokines. Janus Kinases (JAKs) mediate cytokines signaling through the Janus Kinase (JAK)/signal transducer and activator of transcription (STAT) signaling ... ...

Abstract	Rheumatoid Arthritis (RA) is an autoimmune disease caused by overproduction of pro-inflammatory cytokines. Janus Kinases (JAKs) mediate cytokines signaling through the Janus Kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathways. Clinical studies have shown that Janus kinase 1 (JAK1) mediated signaling plays a key role in synovial response in rheumatoid arthritis. Hence, the inhibition JAK1 is considered as an important therapeutic route for treatment of rheumatoid arthritis. In this study, we have performed three-dimensional quantitative structure-activity relationship (3 D-QSAR), molecular docking, molecular dynamics (MD) and free energy calculations on a series of pyrrolo[
MeSH term(s)	Amines ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Quantitative Structure-Activity Relationship
Chemical Substances	Amines
Language	English
Publishing date	2020-01-21
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1714483
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Zs.A 2093: Show issues

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Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation.

Keretsu, Seketoulie / Bhujbal, Swapnil P / Cho, Seung Joo

Scientific reports

2020 Volume 10, Issue 1, Page(s) 17716

Abstract: In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. ... ...

Abstract	In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. The 3C-Like proteinase (3CL
MeSH term(s)	Aclarubicin/chemistry ; Aclarubicin/metabolism ; Aminoisobutyric Acids ; Betacoronavirus/enzymology ; Betacoronavirus/isolation & purification ; Binding Sites ; COVID-19 ; Coronavirus 3C Proteases ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Cysteine Endopeptidases/metabolism ; Databases, Factual ; Humans ; Hydrogen Bonding ; Leucine/analogs & derivatives ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Oligopeptides/chemistry ; Oligopeptides/metabolism ; Pandemics ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; Proline/analogs & derivatives ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Quinolines ; SARS-CoV-2 ; Thermodynamics ; Thiazoles/chemistry ; Thiazoles/metabolism ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Aminoisobutyric Acids ; Oligopeptides ; Protease Inhibitors ; Quinolines ; Thiazoles ; Viral Nonstructural Proteins ; Aclarubicin (74KXF8I502) ; faldaprevir (958X4J301A) ; Proline (9DLQ4CIU6V) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Leucine (GMW67QNF9C)
Keywords	covid19
Language	English
Publishing date	2020-10-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-74468-0
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Article ; Online: Computational study of paroxetine-like inhibitors reveals new molecular insight to inhibit GRK2 with selectivity over ROCK1.

Keretsu, Seketoulie / Bhujbal, Swapnil P / Joo Cho, Seung

Scientific reports

2019 Volume 9, Issue 1, Page(s) 13053

Abstract: The G-protein coupled receptor kinase 2 (GRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. Hence, the inhibition of GRK2 is considered to be an important drug target for ... ...

Abstract	The G-protein coupled receptor kinase 2 (GRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. Hence, the inhibition of GRK2 is considered to be an important drug target for the treatment of heart failure. Due to the high sequence similarity of GRK2 with the A, G, and C family (AGC family) of kinases, the inhibition of GRK2 also leads to the inhibition of AGC kinases such as Rho-associated coiled-coil kinase 1 (ROCK1). Therefore, unraveling the mechanisms to selectively inhibit GRK2 poses an important challenge. We have performed molecular docking, three dimensional quantitative structure activity relationship (3D-QSAR), molecular dynamics (MD) simulation, and free energy calculations techniques on a series of 53 paroxetine-like compounds to understand the structural properties desirable for enhancing the inhibitory activity for GRK2 with selectivity over ROCK1. The formation of stable hydrogen bond interactions with the residues Phe202 and Lys220 of GRK2 seems to be important for selective inhibition of GRK2. Electropositive substituents at the piperidine ring and electronegative substituents near the amide linker between the benzene ring and pyrazole ring showed a higher inhibitory preference for GRK2 over ROCK1. This study may be used in designing more potent and selective GRK2 inhibitors for therapeutic intervention of heart failure.
MeSH term(s)	Algorithms ; Binding Sites ; Catalytic Domain ; Drug Design ; Enzyme Activation/drug effects ; G-Protein-Coupled Receptor Kinase 2/antagonists & inhibitors ; G-Protein-Coupled Receptor Kinase 2/chemistry ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Paroxetine/chemistry ; Paroxetine/pharmacology ; Protein Binding ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology ; Quantitative Structure-Activity Relationship ; rho-Associated Kinases/antagonists & inhibitors ; rho-Associated Kinases/chemistry
Chemical Substances	Protein Kinase Inhibitors ; Paroxetine (41VRH5220H) ; ROCK1 protein, human (EC 2.7.11.1) ; rho-Associated Kinases (EC 2.7.11.1) ; G-Protein-Coupled Receptor Kinase 2 (EC 2.7.11.16)
Language	English
Publishing date	2019-09-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-48949-w
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Article ; Online: Weighted edge based clustering to identify protein complexes in protein-protein interaction networks incorporating gene expression profile.

Keretsu, Seketoulie / Sarmah, Rosy

Computational biology and chemistry

2016 Volume 65, Page(s) 69–79

Abstract: Protein complex detection from protein-protein interaction (PPI) network has received a lot of focus in recent years. A number of methods identify protein complexes as dense sub-graphs using network information while several other methods detect protein ... ...

Abstract	Protein complex detection from protein-protein interaction (PPI) network has received a lot of focus in recent years. A number of methods identify protein complexes as dense sub-graphs using network information while several other methods detect protein complexes based on topological information. While the methods based on identifying dense sub-graphs are more effective in identifying protein complexes, not all protein complexes have high density. Moreover, existing methods focus more on static PPI networks and usually overlook the dynamic nature of protein complexes. Here, we propose a new method, Weighted Edge based Clustering (WEC), to identify protein complexes based on the weight of the edge between two interacting proteins, where the weight is defined by the edge clustering coefficient and the gene expression correlation between the interacting proteins. Our WEC method is capable of detecting highly inter-connected and co-expressed protein complexes. The experimental results of WEC on three real life data shows that our method can detect protein complexes effectively in comparison with other highly cited existing methods. Availability: The WEC tool is available at http://agnigarh.tezu.ernet.in/~rosy8/shared.html.
MeSH term(s)	Cluster Analysis ; Gene Expression Profiling ; Humans ; Protein Interaction Mapping/methods
Language	English
Publishing date	2016-12
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2016.10.001
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