SWISS-MODEL: an automated protein homology-modeling server

By Torsten Schwede, Jürgen Kopp, Nicolas Guex, Manuel C. Peitsch. 2003

5,749 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014, background): “Sequence-based protein alignment and homology detection has been extensively studied and widely applied to many biological problems such as homology modeling [1-4], phylogeny inference [5-7] and protein function prediction [8-10].”
Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, background): “…of a protein can be calculated on the basis of known template structures by homology modeling (Marti-Renom et al., 2000; Petrey and Honig, 2005; Schwede et al., 2003); and atomicandreducedrepresentation modelsofproteincomplexes with small ligands and other macromolecules, such as nucleic…”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “Three other programs that implement this method are 3D-JIGSAW (Bates et al., 2001), RosettaCM (Song et al., 2013), and SWISSMODEL (Schwede et al., 2003).”
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling (2015, methodology): “SWISS-MODEL [10] generates a core model by averaging template backbone atom positions.”
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling (2008, background): “It should be noted that there are Web servers that will also produce homology models, including SwissMode”
Mutations in LRP5 or FZD4 underlie the common familial exudative vitreoretinopathy locus on chromosome 11q. (2004, methodology): “The protein homologymodeling server Swiss-Model (Schwede et al. 2003) was then used to construct the model based on this alignment and the coordinates of the crystal structure of the LDLR YWTD-EGF domain (1n7d chain A) (Rudenko et al. 2002) (fig.”
Embryonic cardiomyocytes beat best on a matrix with heart-like elasticity: scar-like rigidity inhibits beating (2008, methodology): “Based on peptide location, myosin structure (Houdusse et al., 1999; Rayment et al., 1993) and homology modeling (Schwede et al., 2003), structural Journal of Cell Science 121 (22) changes in the myosin head and lever arm were assessed.”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, background): “Therefore, PMP provides a service interface (called “Interactive Modeling”) where to submit target protein sequences to several established modeling services (29, 47, 55, 56, 108) and initiate a new template selection and modeling process for the protein of interest.”
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets (2007, methodology): “21–23 We usually presampled within HADDOCK to obtain an ensemble of starting structures.”
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm (2010, methodology): “All homology modeling was performed using the SWISS-MODEL web server [82] via the so-called ‘‘First Approach mode’’; for oligomeric proteins each individual chain was homology-modeled independently.”
The ProDom database of protein domain families: more emphasis on 3D (2004, methodology): “When 3D structures are available for target domains, the output is directly linked to both SWISS-MODEL ( 17 ) and Geno3D (18) servers for homology-based domain modelling.”
Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells (2007, methodology): “The domains presented were the consensus of folds identified by Composer [53], MatchMaker [54], GeneFold [55], Robetta [56], Fugue [57], and Swiss-Model [58].”