The SWISS-MODEL Workspace: A web-based environment for protein structure modelling

Biozentrum Basel, University of Basel Switzerland.
Bioinformatics (Impact Factor: 4.98). 02/2006; 22(2):195-201. DOI: 10.1093/bioinformatics/bti770
Source: PubMed

ABSTRACT Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases.
SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3.
The SWISS-MODEL workspace can be accessed freely at

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    • "and the NCBI conserved domain database (CDD) (Marchler-Bauer et al., 2011). The tertiary structure of the primary AbTrf protein was generated using the online SWISS model interface (Arnold et al., 2006). In this regard, a 2.60 Å resolution crystal structure of full-length, glycosylated apo-human serotransferrin (hTrF) (PDB no.3V83.1.A.pdb) was selected from the PDB database and used as the template for AbTrf. "
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    ABSTRACT: The basic function of transferrin is to bind iron (III) ions in the medium and to deliver them to the locations where they are required for metabolic processes. It also takes part in the host immune defense mainly via its ability to bind to iron (III) ions. Hence, transferrin is also identified as an important acutephase protein in host immunity. Abalones are major shellfish aquaculture crops that are susceptible to a range of marine microbial infections. Since transferrin is known to be a major player in innate immunity, in the present study we sought to identify, and molecularly and functionally characterize a transferrinlike gene from disk abalone (Haliotis discus discus) named as AbTrf. AbTrf consisted of a 2187-bp open reading frame (ORF) which encodes a 728 amino acid (aa) protein. The putative amino acid sequence of AbTrf harbored N- and C-terminal transferrin-like domains, active sites for iron binding, and conserved cysteine residues. A constitutive tissue specific AbTrf expression pattern was detected by qPCR in abalones where mantle and muscle showed high AbTrf expression levels. Three immune challenge experiments were conducted using Vibrio parahaemolyticus, Listeria monocytogenes and LPS as stimuli and, subsequently, AbTrf mRNA expression levels were quantified in gill and hemocytes in a time-course manner. The mRNA expression was greatly induced in both tissues in response to both challenges. Evidencing the functional property of transferrins, recombinant AbTrf N-terminal domain (AbTrf-N) showed dose-dependent iron (III) binding activity detected by chrome azurol S (CAS) assay system. Moreover, recombinant AbTrf-N could significantly inhibit the growth of iron-dependent bacterium, Escherichia coli in a dose-dependent manner. However, AbTrf-N was unable to show any detectable bacteriostatic activity against iron-independent bacterium Lactobacillus plantarum (L. plantarum) even at its highest concentration. Collectively, our results suggest that AbTrf might play a significant role in the host innate immunity, possibly by withholding iron from pathogens.
    Developmental & Comparative Immunology 11/2015; 53(1):222-233. DOI:10.1016/j.dci.2015.07.013 · 2.82 Impact Factor
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    • "A theoretical three-dimensional model for PDIA3 from T. spiralis was constructed by comparative modelling using the Swiss-Model server, version 3.7 (Arnold et al., 2006; Kiefer et al., 2009; Biasini et al., 2014; http://, which is accessible via the ExPASy web server ( "
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    • "Tertiary structure prediction was performed using SWISS-MODEL online tools (; Schwede et al., 2003; Arnold et al., 2006 "
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    ABSTRACT: Gibberellins (GA) are some of the most important phytohormones involved in plant development. DELLA proteins are negative regulators of GA signaling in many plants. In this study, the full-length cDNA sequences of three DELLA genes were cloned from Artemisia annua. Phylogenetic analysis revealed that AaDELLA1 and AaDELLA2 were located in the same cluster, but AaDELLA3 was not. Subcellular localization analysis suggested that AaDELLAs can be targeted to the nucleus and/or cytoplasm. Real-time PCR indicated that all three AaDELLA genes exhibited the highest expression in seeds. Expression of all AaDELLA genes was enhanced by exogenous MeJA treatment but inhibited by GA3 treatment. Yeast two-hybrid assay showed that AaDELLAs could interact with basic helix-loop-helix transcription factor AaMYC2, suggesting that GA and JA signaling may be involved in cross-talk via DELLA and MYC2 interaction in A. annua.
    Genetics and molecular research: GMR 09/2015; 14(3):10037-49. DOI:10.4238/2015.August.21.10 · 0.78 Impact Factor
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