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Journal ArticleDOI

EasyModeller: A graphical interface to MODELLER

16 Aug 2010-BMC Research Notes (BioMed Central)-Vol. 3, Iss: 1, pp 226-226
TL;DR: The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODEllER and Python preinstalled.
Abstract: MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently. The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way. EasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system.

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Citations
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Journal ArticleDOI
TL;DR: It is found that antiviral treatment led to full recovery of cats when treatment was started at a stage of disease that would be otherwise fatal if left untreated, and results indicate that continuous virus replication is required for progression of immune-mediated inflammatory disease of FIP.
Abstract: Coronaviruses infect animals and humans causing a wide range of diseases. The diversity of coronaviruses in many mammalian species is contributed by relatively high mutation and recombination rates during replication. This dynamic nature of coronaviruses may facilitate cross-species transmission and shifts in tissue or cell tropism in a host, resulting in substantial change in virulence. Feline enteric coronavirus (FECV) causes inapparent or mild enteritis in cats, but a highly fatal disease, called feline infectious peritonitis (FIP), can arise through mutation of FECV to FIP virus (FIPV). The pathogenesis of FIP is intimately associated with immune responses and involves depletion of T cells, features shared by some other coronaviruses like Severe Acute Respiratory Syndrome Coronavirus. The increasing risks of highly virulent coronavirus infections in humans or animals call for effective antiviral drugs, but no such measures are yet available. Previously, we have reported the inhibitors that target 3C-like protease (3CLpro) with broad-spectrum activity against important human and animal coronaviruses. Here, we evaluated the therapeutic efficacy of our 3CLpro inhibitor in laboratory cats with FIP. Experimental FIP is 100% fatal once certain clinical and laboratory signs become apparent. We found that antiviral treatment led to full recovery of cats when treatment was started at a stage of disease that would be otherwise fatal if left untreated. Antiviral treatment was associated with a rapid improvement in fever, ascites, lymphopenia and gross signs of illness and cats returned to normal health within 20 days or less of treatment. Significant reduction in viral titers was also observed in cats. These results indicate that continuous virus replication is required for progression of immune-mediated inflammatory disease of FIP. These findings may provide important insights into devising therapeutic strategies and selection of antiviral compounds for further development for important coronaviruses in animals and humans.

198 citations


Cites background or methods from "EasyModeller: A graphical interface..."

  • ...Three-dimensional structural model of 3CLpro The structural model of FIPV 3CLpro was built based on TGEV 3CLpro (PDB ID: 4F49) [28] using the EasyModeller program (version 4.0) [56] and superimposed on the 3CLpro structure of MERS-CoV (PDB ID: 4WME, teal) [40]....

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  • ...(A) Superimposition of MERS-CoV 3CLpro (PDB ID: 4WME, teal) [40] and FIPV 3CLpro (red) modeled using Modeller [56] based on TGEV 3CLpro as a template (PDB ID: 4F49) [28]....

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  • ...0) [56] and superimposed on the 3CLpro structure of MERS-CoV (PDB ID: 4WME, teal) [40]....

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Journal ArticleDOI
TL;DR: There has been the clarification of protein interactions using 3D structures of proteins that are built with homology modeling, which contributes to the identification of novel drug candidates.
Abstract: Homology modeling is one of the computational structure prediction methods that are used to determine protein 3D structure from its amino acid sequence. It is considered to be the most accurate of the computational structure prediction methods. It consists of multiple steps that are straightforward and easy to apply. There are many tools and servers that are used for homology modeling. There is no single modeling program or server which is superior in every aspect to others. Since the functionality of the model depends on the quality of the generated protein 3D structure, maximizing the quality of homology modeling is crucial. Homology modeling has many applications in the drug discovery process. Since drugs interact with receptors that consist mainly of proteins, protein 3D structure determination, and thus homology modeling is important in drug discovery. Accordingly, there has been the clarification of protein interactions using 3D structures of proteins that are built with homology modeling. This contributes to the identification of novel drug candidates. Homology modeling plays an important role in making drug discovery faster, easier, cheaper, and more practical. As new modeling methods and combinations are introduced, the scope of its applications widens.

190 citations

Journal ArticleDOI
TL;DR: A simple and intuitive interface, PyMod has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks.
Abstract: Background In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users.

135 citations


Cites methods from "EasyModeller: A graphical interface..."

  • ...Up till now, there have been a few attempts earlier to simplify the use of MODELLER by providing a GUI framework (EasyModeller [21], SWIFT MODELLER [22])....

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Journal ArticleDOI
TL;DR: Findings indicate that β-sitosterol improves glycemic control through activation of IR and GLUT4 in the adipose tissue of high fat and sucrose-induced type-2 diabetic rats and can act as potent antidiabetic agent.
Abstract: Adipose tissue is the primary site of storage for excess energy as triglyceride and it helps in synthesizing a number of biologically active compounds that regulate metabolic homeostasis. Consumpti...

114 citations


Cites methods from "EasyModeller: A graphical interface..."

  • ...MODELLER is one of the best and commonly used software for homology modeling of protein three-dimensional structures(Kuntal et al. 2010) The amino acid sequence of the GLUT4 protein from human was retrieved from Swiss-Prot protein sequence database (Bairoch and Apweile 2000)....

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References
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Journal ArticleDOI
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.

46,130 citations


"EasyModeller: A graphical interface..." refers methods in this paper

  • ...The dynamics output binary trajectory files are also saved in the same folder which can be read in by visualization software such as CHIMERA [18] or VMD [19]....

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  • ...Humphrey W, Dalke A, Schulten K: VMD: visual molecular dynamics....

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Journal ArticleDOI
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

35,698 citations

Journal ArticleDOI
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

34,239 citations


"EasyModeller: A graphical interface..." refers background in this paper

  • ...Structural information of biological macromolecules is readily available in the Protein Data Bank (PDB) [1], http://www.pdb.org....

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  • ...The basic template information like its name, chains, heteroatoms, etc are shown in the display area and the CHAIN is automatically set default to the first chain as set in the PDB file....

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  • ...By Sep 2009, the PDB contained ~ 60,713 experimental protein structures that can be grouped into ~ 3500 families [2]....

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  • ...Structural information of biological macromolecules is readily available in the Protein Data Bank (PDB) [1], http://www....

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  • ...As soon as the model is generated, the best model is displayed in the users default PDB viewer like Rasmol [17] as in Fig....

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Journal ArticleDOI
TL;DR: A comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures, which is automated and illustrated by the modelling of trypsin from two other serine proteinases.

12,386 citations