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Frequently, the complete functional units of biological molecules are assemblies of protein and nucleic acid chains. Stunning examples are the complex structures of ribosomes. Here, we present TopMatch-web, a computational tool for the study of the three-dimensional structure, function and evolution of such molecules. The unique feature of TopMatch is its ability to match the protein as well as nucleic acid chains of complete molecular assemblies simultaneously. The resulting structural alignments are visualized instantly using the high-performance molecular viewer NGL. We use the mitochondrial ribosomes of human and yeast as an example to demonstrate the capabilities of TopMatch-web. The service responds immediately, enabling the interactive study of many pairwise alignments of large molecular assemblies in a single session. TopMatch-web is freely accessible at https://topmatch.services.came.sbg.ac.at., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The COPS (Classification Of Protein Structures) web server provides access to the complete repertoire of known protein structures and protein structural domains. The COPS classification encodes pairwise structural similarities as quantified metric relationships. The resulting metrical structure is mapped to a hierarchical tree, which is largely equivalent to the structure of a file browser. Exploiting this relationship we implemented the Fold Space Navigator, a tool that makes navigation in fold space as convenient as browsing through a file system. Moreover, pairwise structural similarities among the domains can be visualized and inspected instantaneously. COPS is updated weekly and stays concurrent with the PDB repository. The server also exposes the COPS classification pipeline. Newly determined structures uploaded to the server are chopped into domains, the locations of the new domains in the classification tree are determined, and their neighborhood can be immediately explored through the Fold Space Navigator. The COPS web server is accessible at http://cops.services.came.sbg.ac.at/.

Unlabelled: The database of known protein structures contains an overwhelming number of structural similarities that frequently point to intriguing biological relationships. The similarities are often difficult to spot, and once detected their comprehension needs proper visualization. Here we introduce the new concept of a Fold Space Navigator, a user interface enabling the efficient navigation through fold space and the instantaneous visualization of pairwise structure similarities., Availability: The Fold Space Navigator is accessible as a public web service at http://services.came.sbg.ac.at

Unlabelled: Progress in structural biology depends on several key technologies. In particular tools for alignment and superposition of protein structures are indispensable. Here we describe the use of the TopMatch web service, an effective computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications. We provide several instructive examples., Availability: TopMatch is available as a public web service at http://services.came.sbg.ac.at.

A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at.

Unlabelled: The database SCOP (Structural Classification Of Proteins) has become a major resource in bioinformatics and protein science. A particular strength of SCOP is the flexibility of its rules enabling the preservation of the many details spotted by experts in the classification process. Here we endow classic SCOP Families with quantified structural information and comment on the structural diversity found in the SCOP hierarchy., Availability: Quantified SCOP (QSCOP) is available as a public WEB service. http://services.came.sbg.ac.at.