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Modeller
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Modeller is the tool of choice for homology modelling based on the multiple templates. The user provides an alignment of a sequence to be modeled with known related structures and Modeller automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints and can perform many additional tasks, including de novo modeling of loops in protein structures. The current service provides an option to use Swiss PDB Viewer project files as an input for Modeller program. The result models can be evalaute with one of several MQA methods. Reference: "A. Sali & T.L. Blundell. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.""

FrankensteinWebOptimizeAlignment
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FRankenstein3D - homology modelling pipeline

RefinerLoop
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The method can be used to refine parts of theoretical protein models that were built without sufficient template structure. The service uses Refiner "de novo" protein structure prediction software based on off-latice, reduced type protein model combined with replica exchange monte carlo sampling. Reference: "Boniecki M, Rotkiewicz P, Skolnick J, Kolinski A. (2003) Protein fragment reconstruction using various modeling techniques. 17(11):725-38"

Crude
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Crude builds crude protein model by copying common coordinates from a template structure. All atoms absent in the template structure are ignored

Scwrl3
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Builds a crude model of a protein by copying common backbone atoms from the template file. Subsequently sidechains are reconstructed with Scwrl3 method. Scwrl3 reference: "A. A. Canutescu, A. A. Shelenkov, and R. L. Dunbrack, Jr. (2003) A graph theory algorithm for protein side-chain prediction. Protein Science 12, 2001-2014 ."

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