The structure assessment web server: for proteins, complexes and more

The structure assessment web server: for proteins, complexes and more

2024 | Andrew M. Waterhouse, Gabriel Studer, Xavier Robin, Stefan Bienert, Gerardo Tauriello and Torsten Schwede
The Structure Assessment web server is a comprehensive tool for evaluating and benchmarking structural models of macromolecular complexes, including proteins and nucleic acids. It provides an interactive web dashboard that integrates sequence and structure information with results from state-of-the-art tools, enabling users to visually explore and assess model quality. The server includes stereochemistry information, secondary structure data, global and local model quality assessments, and membrane location predictions. A benchmarking mode allows comparison of models to reference structures, providing scores used in recent CASP and CAMEO experiments. The server is accessible at https://swissmodel.expasy.org/assess and is integrated within SWISS-MODEL, receiving regular updates since its initial release. It supports a wide range of structural models and offers flexible upload options, including legacy PDB and PDBx/mmCIF formats. The server also allows direct assessment from the SWISS-MODEL workbench and the SWISS-MODEL Repository. The interface includes sequence and 3D viewers, with features such as residue highlighting, color schemes, and interactive exploration. Stereochemistry analysis is provided through Ramachandran plots and MolProbity results. The server also includes a membrane prediction component and quality estimates for theoretical models. Comparison to reference structures is a key feature, with scores for local and global accuracy, interface similarity, and other metrics. The server is free and open to all users, with no login required. It is highly extensible and supports additional features such as protein-ligand interaction analysis. The server is supported by the SIB Swiss Institute of Bioinformatics and the Biozentrum of the University of Basel.The Structure Assessment web server is a comprehensive tool for evaluating and benchmarking structural models of macromolecular complexes, including proteins and nucleic acids. It provides an interactive web dashboard that integrates sequence and structure information with results from state-of-the-art tools, enabling users to visually explore and assess model quality. The server includes stereochemistry information, secondary structure data, global and local model quality assessments, and membrane location predictions. A benchmarking mode allows comparison of models to reference structures, providing scores used in recent CASP and CAMEO experiments. The server is accessible at https://swissmodel.expasy.org/assess and is integrated within SWISS-MODEL, receiving regular updates since its initial release. It supports a wide range of structural models and offers flexible upload options, including legacy PDB and PDBx/mmCIF formats. The server also allows direct assessment from the SWISS-MODEL workbench and the SWISS-MODEL Repository. The interface includes sequence and 3D viewers, with features such as residue highlighting, color schemes, and interactive exploration. Stereochemistry analysis is provided through Ramachandran plots and MolProbity results. The server also includes a membrane prediction component and quality estimates for theoretical models. Comparison to reference structures is a key feature, with scores for local and global accuracy, interface similarity, and other metrics. The server is free and open to all users, with no login required. It is highly extensible and supports additional features such as protein-ligand interaction analysis. The server is supported by the SIB Swiss Institute of Bioinformatics and the Biozentrum of the University of Basel.
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[slides and audio] The structure assessment web server%3A for proteins%2C complexes and more