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


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

135 Reads
  • Source
    • "For homology modelling, the sequence of hpcadherin was retrieved from the NCBI protein sequence database and template was identified using PSI-BLAST against the RCSB protein data bank (PDB). The 3D-structure was built using Swiss- Model server in template mode (Arnold et al., 2006). The modelled structure was subjected to validation and assessment using protein structure and model assessment tools at Swiss-Model server using different estimation patterns. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Anti-epileptic drugs (AEDs) have high risk of teratogenic side effects, including neural tube defects while mother is on AEDs for her own prevention of convulsions during pregnancy. The present study investigated the interaction of major marketed AEDs and human placental (hp)-cadherin protein, insilico, to establish the role of hp-cadherin protein in teratogenicity and also to evaluate the importance of Ca2+ ion in functioning of the protein. A set of 21 major marketed AEDs were selected for the study and 3D-structure of hp-cadherin wa s constructed using homology modelling and energy minimized using MD simulations. Molecular docking studies were carried out using selected AEDs as ligand with hpcadherin (free and bound Ca 2+ ion) to study the behavioural changes in hp-cadherin due to presence of Ca2+ ion. The study refl ected that four AEDs (Gabapentin, Pregabalin, Remacimide and Vigabatrine) had very high affinity towards hp-cadherin and thus the later may have prominent role in the teratogenic effects of these AEDs. From docking simulation analysis it wa s observed that Ca2+ ion is required to make hp-cadherin energetically favourable and sterically functional.
    Computational Biology and Chemistry 11/2016; 60:1-8. DOI:10.1016/j.compbiolchem.2015.11.003 · 1.12 Impact Factor
  • Source
    • "Models were compared with those produced with Swiss-Model (Arnold et al., 2006) and RaptorX (Kallberg et al., 2012). Structural alignments were refined by visual inspection and using the secondary-structure (SSM) server (Krissinel and Henrick, 2004). "
    [Show abstract] [Hide abstract]
    ABSTRACT: A double homozygous atc1Δ /atc1Δ /ntc1Δ /ntc1Δ mutant (atc1Δ /ntc1Δ KO) was constructed in the pathogen opportunistic yeast Candida parapsilosis by disruption of the two chromosomal alleles coding for NTC1 gene (encoding a neutral trehalase) in a Cpatc1Δ /atc1Δ background (atc1Δ KO strain, deficient in acid trehalase). The Cpatc1Δ /ntc1Δ KO mutant failed to counteract the inability of Cpatc1Δ cells to metabolize exogenous trehalose and showed a similar growth pattern on several monosaccharides and disaccharides. However, upon prolonged incubation in either rich medium (YPD) or nutrient-starved medium the viability of Cpatc1Δ cells exhibited a sensitive phenotype, which was augmented by further CpNTC1/NTC1 disruption. Furthermore, Cpatc1Δ /ntc1Δ KO cells had difficulty in resuming active growth in fresh YPD. This homozygous mutant also lacked any in vitro measurable trehalase activity, whether acid or neutral, suggesting that a single gene codes for each enzyme. By contrast, in Cpatc1Δ /ntc1Δ KO strain the resistance to oxidative and heat stress displayed by atc1Δ mutant was suppressed. Cpatc1Δ /ntc1Δ KO cells showed a significant decrease in virulence as well as in the capacity to form biofilms. These results point to a major role for acid trehalase (Atc1p) in the pathobiology of C. parapsilosis, whereas the activity of neutral trehalase can only partially counteract Atc1p deficiency. They also support the use of ATC1 and NTC1 genes as interesting antifungal targets.
    Fungal Genetics and Biology 11/2015; 85. DOI:10.1016/j.fgb.2015.10.007 · 2.59 Impact Factor
  • Source
    • " (Arnold et al., 2006) based on the homology model with Homo sapiens Cu,Zn-SOD (Ref. PDB ID: 4B3E) (Strange et al., 2012), which showed the highest sequence identity of 76.97%. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Superoxide dismutase (SOD, EC is an antioxidant enzyme found in all living cells. It regulates oxidative stress by breaking down superoxide radicals to oxygen and hydrogen peroxide. A gene coding for Cu,Zn-SOD was cloned and characterized from Siamese crocodile (Crocodylus siamensis; CSI). The full-length expressed sequence tag (EST) of this Cu,Zn-SOD gene (designated as CSI-Cu,Zn-SOD) contained 462 bp encoding a protein of 154 amino acids without signal peptides, indicated as intracellular CSI-Cu,Zn-SOD. This agreed with the results from the phylogenetic tree, which indicated that CSI-Cu,Zn-SOD belonged to the intracellular Cu,Zn-SOD. Chromosomal location determined that the CSI-Cu,Zn-SOD was localized to the proximal region of the Siamese crocodile chromosome 1p. Several highly conserved motifs, two conserved signature sequences (GFHVHEFGDNT and GNAGGRLACGVI), and conserved amino acid residues for binding copper and zinc (His(47), His(49), His(64), His(72), His(81), Asp(84), and His(120)) were also identified in CSI-Cu,Zn-SOD. Real-time PCR analysis showed that CSI-Cu,Zn-SOD mRNA was expressed in all the tissues examined (liver, pancreas, lung, kidney, heart, and whole blood), which suggests a constitutively expressed gene in these tissues. Expression of the gene in Escherichia coli cells followed by purification yielded a recombinant CSI-Cu,Zn-SOD, with Km and Vmax values of 6.075 mM xanthine and 1.4×10(-3) mmol min (-1)mg (-1), respectively. This Vmax value was 40 times lower than native Cu,Zn-SOD (56×10(-3) mmol min (-1)mg (-1)), extracted from crocodile erythrocytes. This suggests that cofactors, protein folding properties, or post-translational modifications were lost during the protein purification process, leading to a reduction in the rate of enzyme activity in bacterial expressed CSI-Cu,Zn-SOD.
    Comparative biochemistry and physiology. Part A, Molecular & integrative physiology 11/2015; 191. DOI:10.1016/j.cbpa.2015.10.028 · 1.97 Impact Factor
Show more