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Genomes and their proteins can be analyzed by different perspectives, with different goals and applicability of results in several areas of research. In bioinformatics and computational biology, it is common the use of multiple combinations of programs and databases to extract information from the raw data. Choosing the proper program, setting its parameters, filtering the input files, extracting information from output files, and creating scripts for automating tasks can be challenging. This work describes the MHOLline, an online scientific workflow that provides a set of modules that enables a broad large-scale analysis of proteins (e.g. whole genomes) in a few hours. The version 1.0 (released in 2010), was wholly reformulated, and the new version 2.0 is available at www.mholline2.lncc.br. This version presents new features, modules, interface, code optimization, runtime reduction, more security, a new results visualization interface, and an automatic and user-friendly refinement page

MHOLline 2.0: Workflow for automatic large-scale modeling and analysis of proteins