There is an increasing gap between the number of known protein sequences and the number of proteins with experimentally characterized structure and function. To alleviate this issue, we have developed the I-TASSER gateway, an online server for automated and reliable protein structure and function prediction. For a given sequence, I-TASSER starts with template recognition from a known structure library, followed by full-length atomic model construction by iterative assembly simulations of the continuous structural fragments excised from the template alignments. Functional insights are then derived from comparative matching of the predicted model with a library of proteins with known function. The I-TASSER pipeline has been recently integrated with the XSEDE Gateway system to accommodate pressing demand from the user community and increasing computing costs. This report summarizes the configuration of the I-TASSER Gateway with the XSEDE-Comet supercomputer cluster, together with an overview of the I-TASSER method and milestones of its development.
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| http://dx.doi.org/10.1016/j.future.2019.04.011 | DOI Listing |
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I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.
Future Gener Comput Syst
October 2019
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, United States.
There is an increasing gap between the number of known protein sequences and the number of proteins with experimentally characterized structure and function. To alleviate this issue, we have developed the I-TASSER gateway, an online server for automated and reliable protein structure and function prediction. For a given sequence, I-TASSER starts with template recognition from a known structure library, followed by full-length atomic model construction by iterative assembly simulations of the continuous structural fragments excised from the template alignments.
View Article and Find Full Text PDFHistatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses.
Sci Rep
January 2014
1] Department of Periodontics, College of Dentistry, The University of Iowa, Iowa City, IA 52242, USA [2] Dows Institute for Dental Research, College of Dentistry, The University of Iowa, Iowa City, IA 52242, USA.
Histatins are human salivary gland peptides with anti-microbial and anti-inflammatory activities. In this study, we hypothesized that histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and attenuates HagB-induced chemokine responses in human myeloid dendritic cells. Histatin 5 bound to immobilized HagB in a surface plasmon resonance (SPR) spectroscopy-based biosensor system.
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