The PSIPRED protein structure prediction server

McGuffin, Liam J.; Bryson, Kevin; Jones, David T.

doi:10.1093/bioinformatics/16.4.404

Cited by 3,347 publications

(2,530 citation statements)

References 13 publications

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“…This protein sequence was studied through several bioinformatics tools for the present study. The secondary structure of the E2 protein was analyzed with Psipred [23] (http://bioinf.cs.ucl.ac.uk/psipred/). Protein glycosylation is important for secretion, localization and stability of the protein.…”

Section: Sequence Analysismentioning

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: Sequence Analysismentioning

confidence: 99%

“…The secondary structure image (Fig. 3) was generated using Psipred [23] (http://bioinf.cs. ucl.ac.uk/psipred/).…”

Section: Sequence Propertiesmentioning

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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“…Identical residues are shown in reverse font and functionally conserved residues are shown with gray background. The predicted secondary structure elements [58] of S. mansoni NPC2 are shown above the sequence alignment. Predicted β-sheets (arrows) and leader peptide (tube) are indicated.…”

Section: Supplementary Materialsmentioning

confidence: 99%

Proteomic analysis of Schistosoma mansoni egg secretions

Cass

Johnson

Califf

et al. 2007

Molecular and Biochemical Parasitology

194

196

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Schistosomiasis remains a largely neglected, global health problem. The morbid pathology of the disease stems from the host's inflammatory response to parasite eggs trapped in host tissues. Long term host/parasite survival is dependent upon the successful modulation of the acute pathological response, which is induced by egg antigens. In this study, using Multidimensional Protein Identification Technology, we identified the Schistosoma mansoni egg secretome consisting of 188 proteins. Notably we identified proteins involved in redox balance, molecular chaperoning and protein folding, development and signaling, scavenging and metabolic pathways, immune response modulation, and 32 novel, previously uncharacterized schistosome proteins. We localized a subset of previously-characterized schistosome proteins identified in egg secretions in this study, to the surface of live S. mansoni eggs using the circumoval precipitin reaction. The identification of proteins actively secreted by live schistosome eggs provides important new information for understanding immune modulation and the pathology of schistosomiasis.

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“…For this purpose, AutoLink makes use of the parameters presented by Wang and Jardetzky [22] which can take predicted secondary structure into account. The secondary structure prediction can be done using any program [23][24][25] and the predictions are easily incorporated into AutoLinkÕs calculations through its graphical interface. Alternatively, AutoLink can be instructed to simply use secondarystructure-and/or nearest-neighbor-independent empirically defined average chemical shift values.…”

Section: Score Thresholdmentioning

confidence: 99%

AutoLink: Automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic

Masse

Keller

2005

Journal of Magnetic Resonance

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We have developed a new computer algorithm for determining the backbone resonance assignments for biopolymers. The approach we have taken, relative hypothesis prioritization, is implemented as a Lua program interfaced to the recently developed computer-aided resonance assignment (CARA) program. Our program can work with virtually any spectrum type, and is especially good with NOESY data. The results of the program are displayed in an easy-to-read, color-coded, graphic representation, allowing users to assess the quality of the results in minutes. Here we report the application of the program to two RNA recognition motifs of Apobec-1 Complementation Factor. The assignment of these domains demonstrates AutoLinkÕs ability to deliver accurate resonance assignments from very minimal data and with minimal user intervention.

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The PSIPRED protein structure prediction server

Abstract: Freely available to non-commercial users at http://globin.bio.warwick.ac.uk/psipred/

Cited by 3,347 publications

References 13 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

Proteomic analysis of Schistosoma mansoni egg secretions

AutoLink: Automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic

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