The PSIPRED Protein Analysis Workbench is a new web-based platform developed by the UCL Bioinformatics Group, offering a unified framework for various protein analysis methods. The platform provides a streamlined user interface with enhanced features, allowing users to explore their results more effectively. It includes additional services for scalable execution of prediction methods, such as SOAP and XML-RPC web server access and HADOOP packages. All software and services are available at http://bioinf.cs.ucl.ac.uk/. The workbench integrates a range of sequence and structure annotation methods, including PSIPRED, GenTHREADER, pGenTHREADER, pDomTHREADER, MEMSAT-SVM/MEMSAT3, MEMPACK, BioSerf, MetSite, HSPred, DISOPRED2, DomPred, and FFPred. BioSerf v2.0 is a fully automated homology modelling protocol that uses multiple methods to generate and assess homology models. FFPred v2.0 performs feature-based function prediction and assigns Gene Ontology (GO) classes to query sequences using support vector machines (SVMs). It now includes 442 GO classes and assigns reliability labels to predictions based on classifier performance. MEMSAT-SVM is an SVM-based transmembrane topology predictor that can automatically identify pore-lining regions in transmembrane proteins. HSPred is an SVM-based method that identifies residues in protein-protein interfaces that contribute most to binding free energy. HADOOP packages have been developed to enable high-throughput execution of key methods like pGenTHREADER, PSIPRED, and DISOPRED on cloud services. The new web server provides two main portals: the Protein Analysis Workbench and the Structure Analysis Workbench. These portals allow users to select multiple analyses and explore results. The server has been optimized to minimize the number of PSIBLAST jobs, improving efficiency. Results pages are now tab-based, allowing users to explore detailed outputs and download files. SOAP/XML-RPC access is available for programmatic use, enabling automated analysis. The platform also supports re-submitting sub-sequences for further analysis, facilitating complex workflows. A use case demonstrates how the workbench can be used to analyze a mouse protein, identifying potential domain boundaries and structural features. The PSIPRED workbench offers a range of accurate protein prediction methods and software, accessible via the web or for local use. It supports scalable analysis through web services, HADOOP packages, and cloud computing. The platform is essential for computational biology in the post-genomic era, providing tools for protein annotation and analysis. Funding for open access is provided by the Biotechnology and Biological Sciences Research Council (BBSRC).The PSIPRED Protein Analysis Workbench is a new web-based platform developed by the UCL Bioinformatics Group, offering a unified framework for various protein analysis methods. The platform provides a streamlined user interface with enhanced features, allowing users to explore their results more effectively. It includes additional services for scalable execution of prediction methods, such as SOAP and XML-RPC web server access and HADOOP packages. All software and services are available at http://bioinf.cs.ucl.ac.uk/. The workbench integrates a range of sequence and structure annotation methods, including PSIPRED, GenTHREADER, pGenTHREADER, pDomTHREADER, MEMSAT-SVM/MEMSAT3, MEMPACK, BioSerf, MetSite, HSPred, DISOPRED2, DomPred, and FFPred. BioSerf v2.0 is a fully automated homology modelling protocol that uses multiple methods to generate and assess homology models. FFPred v2.0 performs feature-based function prediction and assigns Gene Ontology (GO) classes to query sequences using support vector machines (SVMs). It now includes 442 GO classes and assigns reliability labels to predictions based on classifier performance. MEMSAT-SVM is an SVM-based transmembrane topology predictor that can automatically identify pore-lining regions in transmembrane proteins. HSPred is an SVM-based method that identifies residues in protein-protein interfaces that contribute most to binding free energy. HADOOP packages have been developed to enable high-throughput execution of key methods like pGenTHREADER, PSIPRED, and DISOPRED on cloud services. The new web server provides two main portals: the Protein Analysis Workbench and the Structure Analysis Workbench. These portals allow users to select multiple analyses and explore results. The server has been optimized to minimize the number of PSIBLAST jobs, improving efficiency. Results pages are now tab-based, allowing users to explore detailed outputs and download files. SOAP/XML-RPC access is available for programmatic use, enabling automated analysis. The platform also supports re-submitting sub-sequences for further analysis, facilitating complex workflows. A use case demonstrates how the workbench can be used to analyze a mouse protein, identifying potential domain boundaries and structural features. The PSIPRED workbench offers a range of accurate protein prediction methods and software, accessible via the web or for local use. It supports scalable analysis through web services, HADOOP packages, and cloud computing. The platform is essential for computational biology in the post-genomic era, providing tools for protein annotation and analysis. Funding for open access is provided by the Biotechnology and Biological Sciences Research Council (BBSRC).