The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
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/
BMC Biotechnology 12/2015; 15(1). DOI:10.1186/s12896-015-0135-y · 2.59 Impact Factor
Orphanet Journal of Rare Diseases 12/2015; 10(1). DOI:10.1186/s13023-015-0244-7 · 3.96 Impact Factor
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ABSTRACT: Background Mercury (Hg) is not only a threat to public health but also a growth risk factor to plants, as it is readily accumulated by higher plants. Accumulation of Hg in plants disrupts many cellular-level functions and inhibits growth and development; however, the detoxification and tolerance mechanisms of plants to Hg stress are still not fully understood. Exposure to toxic Hg also occurs in some crops cultivated under anoxic conditions, such as rice (Oryza sativa L.), a model organism and one of the most important cultivated plants worldwide. In this study, we functionally characterized a rice translationally controlled tumor protein gene (Os11g43900, OsTCTP) involved in Hg stress tolerance. Results OsTCTP was ubiquitously expressed in all examined plant tissues, especially in actively dividing and differentiating tissues, such as roots and nodes. OsTCTP was found to localize both the cytosol and the nucleus. OsTCTP was induced by mercuric chloride, cupric sulfate, abscisic acid, and hydrogen peroxide at the protein level in a time-dependent manner. Overexpression of OsTCTP potentiated the activities of several antioxidant enzymes, reduced the Hg-induced H2O2 levels, and promoted Hg tolerance in rice, whereas knockdown of OsTCTP produced opposite effects. And overexpression of OsTCTP did not prevent Hg absorption and accumulation in rice. We also demonstrated that Asn 48 and Asn 97 of OsTCTP amino acids were not the potential N-glycosylation sites. Conclusions Our results suggest that OsTCTP is capable of decreasing the Hg-induced reactive oxygen species (ROS), therefore, reducing the damage of ROS and enhancing the tolerance of rice plants to Hg stress. Thus, OsTCTP is a valuable gene for genetic engineering to improve rice performance under Hg contaminated paddy soils. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0500-y) contains supplementary material, which is available to authorized users.BMC Plant Biology 05/2015; 15(1). DOI:10.1186/s12870-015-0500-y · 3.94 Impact Factor