Multicom ((FULL))
Gwen Simon
Prediction of the three-dimensional (3D) structure of a protein from its sequence is important for studying its biological function. With the advancement in deep learning contact distance prediction and residue-residue coevolutionary analysis, significant progress has been made in both template-based and template-free protein structure prediction in the last several years. Here, we provide a practical guide for our latest MULTICOM protein structure prediction system built on top of the latest advances, which was rigorously tested in the 2018 CASP13 experiment. Its specific functionalities include: (1) prediction of 1D structural features (secondary structure, solvent accessibility, disordered regions) and 2D interresidue contacts; (2) domain boundary prediction; (3) template-based (or homology) 3D structure modeling; (4) contact distance-driven ab initio 3D structure modeling; and (5) large-scale protein quality assessment enhanced by deep learning and predicted contacts. The MULTICOM web server ( _cluster/ ) presents all the 1D, 2D, and 3D prediction results and quality assessment to users via user-friendly web interfaces and e-mails. The source code of the MULTICOM package is also available at -toolbox/multicom .
In order to facilitate the use of the tools, the user manuals for these tools have been developed in PDF and HTML format and are available at the MULTICOM web site. The user manuals usually include step-by-step installation instructions, application examples, references to more technical documents, and frequently asked questions (FAQ) and solutions. In order to better serve users and gather community feedback to improve the toolbox, a mailing list is created. After subscribing the MULTICOM mailing list (multicom...@googlegroups.com), a user can post a message to the mailing list and view the collection of all prior postings. The technical support of the MULTICOM toolbox regularly reads the message postings and answers questions. Collected improvements will be released in future versions of the toolbox.
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