Swiss-PDB Viewer (Deep View)

Kaplan, Warren; Littlejohn, Timothy G.

doi:10.1093/bib/2.2.195

Cited by 413 publications

(235 citation statements)

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“…The selected model was refined using CHARMm [45] and energy minimization was done using ChiRotor algorithm of DS. The GROMOS [44] algorithm implemented in DeepView [19] was used for energy minimization of the predicted E2 structure. The three dimensional models were validated by PROCHECK in SAVeS server [21,22].…”

Section: Structure Prediction and Validationmentioning

confidence: 99%

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Potential entry inhibitors of the envelope protein (E2) of Chikungunya virus: in silico structural modeling, docking and molecular dynamic studies

et al. 2017

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Chikungunya fever is an arboviral infection caused by the Chikungunya virus (CHIKV) and is transmitted by Aedes mosquito. The envelope protein (E2) of Chikungunya virus is involved in attachment of virion with the host cell. The present study was conceptualized to determine the structure of E2 protein of CHIKV and to identify the potential viral entry inhibitors. The secondary and tertiary structure of E2 protein was determined using bioinformatics tools. The mutational analysis of the E2 protein suggested that mutations may stabilize or de-stabilize the structure which may affect the structure-function relationship. In silico screening of various compounds from different databases identified two lead molecules i.e. phenothiazine and bafilomycin. Molecular docking and MD simulation studies of the E2 protein and compound complexes was carried out. This analysis revealed that bafilomycin has high docking score and thus high binding affinity with E2 protein suggesting stable protein-ligand interaction. Further, MD simulations suggested that both the compounds were stabilizing E2 protein. Thus, bafilomycin and phenothiazine may be considered as the lead compounds in terms of potential entry inhibitor for CHIKV. Further, these results should be confirmed by comprehensive cell culture, cytotoxic assays and animal experiments. Certain derivatives of phenothiazines can also be explored in future studies for entry inhibitors against CHIKV. The present investigation thus provides insight into protein structural dynamics of the envelope protein of CHIKV. In addition the study also provides information on the dynamics of interaction of E2 protein with entry inhibitors that will contribute towards structure based drug design.

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Section: Structure Prediction and Validationmentioning

confidence: 99%

“…Various methods were used for the prediction of the effect of mutations on the structure of E2 protein. Swiss-PDB Viewer [19] was used to generate the structural mutants. The structural stability of wild type and mutant E2 protein were compared using the SDM server (Site Directed Mutator).…”

Section: Mutation Analysismentioning

confidence: 99%

Potential entry inhibitors of the envelope protein (E2) of Chikungunya virus: in silico structural modeling, docking and molecular dynamic studies

et al. 2017

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“…The first one showed good interactions in the active site of ABL kinase and the second one for the T315I ABL kinase. After the preparation of the ligands in Autodock Tools, these X-ray structures were analyzed using Swiss PDB viewer [22] in order to find and correct any errors and to model any missing atoms, and after their minimized states were calculated using the AMBER force field in GROMACS adding polar hydrogens throughout the structures. Then, Kollman charges were added using Autodock Tools, and .pdbqt formats were generated for the docking calculations.…”

Section: Docking Receptor Preparationmentioning

confidence: 99%

<strong>Docking studies of 1,5-disubtituted tetrazoles analogs of the anticancer drug imatinib as probable inhibitors of the ABL kinase and the T315I mutant kinase </strong>

Cortés-García

Suárez-Castro

Gamez-Montaño

et al. 2017

Proceedings of the 21st International Electronic Conference on Synthetic Organic Chemistry

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Abstract:A docking studies of a set of several 1,5-disubstituted tetrazoles (1,5-DS-T) compounds to find potential inhibitors of the Abelson tyrosine-protein kinase (ABL kinase) and the mutated ABL kinase T315I were conducted by using Lamarckian genetic algorithms as search algorithms in Autodock4. Bayesian calculations were performed, and specificity (Sp) and sensitivity (Se) values as well as positive predicted values (PPVs) and negative predicted values (NPVs) were calculated using a set of 99 active ligands and 385 decoys for ABL kinase from the DUD database. RMSD values were calculated between the X-ray crystallographically determined coordinates of the ligands in the complexes of ligand with the ABL kinase and with T315I ABL kinase resistant to imatinib. The predicted results showed the importance of the interactions of the protein with halogens present in some of these 1,5-DS-T ligands. In conclusion, the results suggest that eight novel 1,5-DS-T compounds were identified to be effective inhibitors of ABL kinase.

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“…For the submitted sequences, five 3D models were obtained and considering the lowest energy the best model was selected. Furthermore, the mutant structures were made as a point mutations in native proteins at C.G2901T (P.C634F) (cysteine to phenylalanine), C.G2901A (P.C634Y) (cysteine to tyrosine) and C.G2251A (p.G691S) (glycine to serine) using SPDB viewer (Kaplan et al, 2001). The wild-type and mutant structures were energetically optimized by applying the all atom OPLS force field available under the GROMACS 4.5 package (Pronk et al, 2013).…”

Section: Modeling Of Wild-type and Mutant Retmentioning

confidence: 99%

Characterization of Wild-Type and Mutated RET Proto-Oncogene Associated with Familial Medullary Thyroid Cancer

Masbi¹,

Mohammadi-Asl²,

Galehdari³

et al. 2014

Asian Pacific Journal of Cancer Prevention

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Background: We aimed to assess RET proto-oncogene polymorphisms in three different Iranian families with medullary thyroid cancer (MTC), and performed molecular dynamics simulations and free energy stability analysis of these mutations. Materials and Methods: This study consisted of 48 patients and their first-degree relatives with MTC confirmed by pathologic diagnosis and surgery. We performed molecular dynamics simulations and free energy stability analysis of mutations, and docking evaluation of known RET proto-oncogene inhibitors, including ZD-6474 and ponatinib, with wild-type and mutant forms. Results: The first family consisted of 27 people from four generations, in which nine had the C.G2901A (P.C634Y) mutation; the second family consisted of six people, of whom three had the C.G2901T (P.C634F) mutation, and the third family, who included 12 individuals from three generations, three having the C.G2251A (P.G691S) mutation. The automated 3D structure of RET protein was predicted using I-TASSER, and validated by various protein model verification programs that showed more than 96.3% of the residues in favored and allowed regions. The predicted instability indices of the mutated structures were greater than 40, which reveals that mutated RET protein is less thermo-stable compared to the wild-type form (35.4). Conclusions: Simultaneous study of the cancer mutations using both in silico and medical genetic procedures, as well as onco-protein inhibitor binding considering mutation-induced drug resistance, may help in better overcoming chemotherapy resistance and designing innovative drugs.

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Swiss-PDB Viewer (Deep View)

Cited by 413 publications

References 0 publications

Potential entry inhibitors of the envelope protein (E2) of Chikungunya virus: in silico structural modeling, docking and molecular dynamic studies

Potential entry inhibitors of the envelope protein (E2) of Chikungunya virus: in silico structural modeling, docking and molecular dynamic studies

<strong>Docking studies of 1,5-disubtituted tetrazoles analogs of the anticancer drug imatinib as probable inhibitors of the ABL kinase and the T315I mutant kinase </strong>

Characterization of Wild-Type and Mutated RET Proto-Oncogene Associated with Familial Medullary Thyroid Cancer

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