Article

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

Universität Basel, Bâle, Basel-City, 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 http://swissmodel.expasy.org/workspace/

Download full-text

Full-text

Available from: Lorenza Bordoli, Dec 10, 2015
  • Source
    • "Neither P. falciparum SWIB/MDM2 domains has been crystallized. Predicted tertiary structures were generated using several online tools—the Swiss Model Workspace Automatic Modelling Mode[23], PHYRE2[24]and ESyPred3D Web Server 1.0[25]. Predictions were made relative to the server's inherent template databases or to user-defined templates. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background: Malaria remains a global health problem and the majority of deaths are caused by Plasmodium falciparum parasites. Due to the rapid emergence of drug-resistant strains, novel avenues of research on the biology of the parasite are needed. The massive proliferation of asexual, intra-erythrocytic parasites every 48 h could kill the human host prior to transmission of slow-developing gametocytes to the mosquito vector. A self-induced P. falciparum programmed cell death mechanism has been hypothesized to maintain this balance between the parasite and its two hosts, but molecular participants of the cell death pathway in P. falciparum have not been characterized. Proteins with SWIB/MDM2 domains play a key role in metazoan programmed cell death and this study provides the first evaluation of two parasite SWIB/MDM2 homologues, PF3D7_0518200 (PfMDM2) and PF3D7_0611400 (PfSWIB). Methods: The function of these proteins was assessed by predicting their structural topology with the aid of bioinformatics and determining their location within live transgenic parasites, expressing green fluorescent protein-tagged PfMDM2 and PfSWIB under normal and elevated temperatures, which mimic fever and which are known to induce a programmed cell death response. Additionally, P. falciparum phage display library technology was used to identify binding partners for the two parasite SWIB/MDM2 domains. Results: Structural features of the SWIB/MDM2 domains of PfMDM2 and PfSWIB, suggested that they are chromatin remodelling factors. The N-terminal signal sequence of PfMDM2 directed the protein to the mitochondrion under both normal and heat stress conditions. Plasmodium falciparum phage display library technology revealed that the C-terminal SWIB/MDM2 domain of PfMDM2 interacted with a conserved protein containing a LisH domain. PfSWIB localized to the cytoplasm under normal growth conditions, while approximately 10 % of the heat-stressed trophozoite-stage parasites presented a rapid but short-lived nuclear localization pattern. Two PfSWIB binding partners, a putative Aurora-related kinase and a member of the inner membrane complex, were identified. Conclusion: These novel data provide insight into the function of two parasite SWIB/MDM2 homologues and suggest that PfMDM2 plays a role within the mitochondrion and that PfSWIB is involved in a stage-specific, heat-stress, response pathway.
    Preview · Article · Dec 2016 · Malaria Journal
  • 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.
    Full-text · Article · Nov 2016 · Computational Biology and Chemistry
  • Source
    • "Spatial restrictions were applied to ensure that the best model of each defensing was selected according to DOPE energy. The quality of these models was evaluated according to 3D alignment and energy via the Root Mean Square Deviation (RMSD) and Atomic Non-Local Environment Assessment (Arnold et al., 2006). "

    Full-text · Article · Feb 2016 · Genetics and molecular research: GMR
Show more