EasyModeller: A graphical interface to MODELLER

Kuntal, Bhusan K.; Aparoy, Polamarasetty; Reddanna, Pallu

doi:10.1186/1756-0500-3-226

Cited by 207 publications

(131 citation statements)

References 19 publications

(15 reference statements)

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“…The predicted secondary structure, putative posttranslational modifications, as well as the function of the residues and best templates, were obtained using the tools available in ExPASy [Gasteiger et al, 2003]. Tertiary structures of the kinase domain of PINK1 were obtained and optimized using default settings in EasyModeller [Kuntal et al, 2010] with Modeller 9v7 [Eswar et al, 2008]. As templates were used three proteins from Homo sapiens: Calmodulin dependent kinase II (pdb ID: 2v7oA; MIM] 114078), FLT3 (receptor tyrosine kinase, pdb ID: 1rjbA), and Protein Kinase Ct (pdb ID: 2jedA) and one from Toxoplasma gondii: Calmodulin dependent kinase 3 (pdb ID: 3hztA).…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

et al. 2011

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Parkinson disease (PD) is the second most common neurodegenerative disorder and is characterized by the loss of dopaminergic neurons in the substantia nigra. Mutations in PINK1 were shown to cause recessive familial PD, and today are proposed to be associated with the disease via mitochondrial dysfunction and oxidative damage. The PINK1 gene comprises eight exons, which encode a ubiquitously expressed 581 amino acid protein that contains an N-terminal mitochondrial targeting domain and a serine/threonine protein kinase. To better understand the relationship between PINK1 and PD we have first analyzed the evolutionary history of the gene showing its late emergence in evolution. In addition, we have modeled the three-dimensional structure of PINK1 and found some evidences that help to explain the effect of some PD-related mutations in this protein's function.

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Section: Methodsmentioning

confidence: 99%

Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

et al. 2011

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“…The only con of it is that it is command line based where the users find it a bit difficult to start with it [7].…”

Section: Toolsmentioning

confidence: 99%

Molecular Modeling and Docking Study of 2-Nitropropane Dioxygenase of Mycobacterium tuberculosis

Am¹,

Ibrahim²,

Yadav³

et al. 2017

Int J Biomed Data Min

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Mycobacterium tuberculosis is infectious bacteria and causes tuberculosis in humans. M. tuberculosis infects the immune deficient human and shows the symptoms of the infection. Also bacteria stay in latent phase inside the human body and can be active in suitable conditions. One third of the total population of the world is infected by M. tuberculosis; therefore it is very important to have potential drugs against tuberculosis. Mycobacteria have reported multidrug resistance to the available drugs for tuberculosis. Hence, there is a need to find a new target for the drugs. Fatty acid synthase II (FAS II) is the enzyme that catalyzes the synthesis of fatty acid and is not found in humans. It is a multifunctional polypeptide, composed of different domains in which can be targeted individually to inhibit the function of FAS II. 2-Nitropropane Dioxygenase is a part of enoyl reductase domain in FAS II and can be potentially targeted. In this study, the homology modeling of 2NPD from M. tuberculosis has been done and small molecules that have the potential to bind and inhibit the function of the enzyme have been identified. Also the stability of proteinligand complex was determined.

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“…The comparative modeling was conducted using EasyModeller 4.0 [9]. A sequence of P. falciparum GGPPS, which had been downloaded from UniProt as a FASTA file (Q86GK8), was employed as the query.…”

Section: Comparative Modelingmentioning

confidence: 99%

Predicted Binding Mode of Andrographolide and Its Derivatives Bound to Plasmodium Falciparum Geranylgeranyl Pyrophosphate Synthase

Putra

Chaidir²,

Hanafi

et al. 2017

Int J App Pharm

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Objective: Andrographolide is a major secondary metabolite in the Indonesian herb sambiloto (Andrographis paniculata). It displays a moderate antiplasmodial activity against the chloroquine-resistant strain of Plasmodium falciparum. This study aimed to investigate andrographolide inhibition of geranylgeranyl pyrophosphate synthase (GGPPS) by andrographolide molecular docking.Methods: A comparative modeling of P. falciparum GGPPS was conducted using one of the Plasmodium vivax GGPPS crystal structures as a template. The best model from this comparative modeling was then used in a molecular docking to investigate the binding mode of andrographolide in the P. falciparum GGPPS active site. Results:In the P. falciparum GGPPS active site, andrographolide is situated with its double rings pointing toward the hydrophobic pocket, while its lactone group is positioned between first aspartate-rich motif and second aspartate-rich motif of the catalytic pocket. Conclusions:In the active site, andrographolide is situated with its double rings pointing toward the hydrophobic pocket, while its lactone group is positioned in the catalytic pocket.

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EasyModeller: A graphical interface to MODELLER

Cited by 207 publications

References 19 publications

Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

Phylogenetic and in silico structural analysis of the Parkinson disease‐related kinase PINK1

Molecular Modeling and Docking Study of 2-Nitropropane Dioxygenase of Mycobacterium tuberculosis

Predicted Binding Mode of Andrographolide and Its Derivatives Bound to Plasmodium Falciparum Geranylgeranyl Pyrophosphate Synthase

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