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Content with tag computational chemistry .

Webinar: Gateway Showcase featuring I-TASSER and Chem Compute

September 13, 2017

Gateway Showcase featuring

I-TASSER
Presented by Chengxin Zhang, Department of Computational Medicine and Bioinformatics, University of Michigan

and

Chem Compute
Presented by Mark Perri, Assistant Professor of Chemistry, Sonoma State University

Details

I-TASSER Science Gateway for Protein Structure and Function Prediction
Chengxin Zhang, S. M. Mortuza, and Yang Zhang
Department of Computational Medicine and Bioinformatics, University of Michigan

Abstract: I-TASSER (Iterative Threading ASSembly Refinement) is a composite method for atomic-level protein structure prediction and structure-based protein function annotation. The on-line server system has been widely used by the biomedical community with registered users coming from more than 130 countries. In Fall 2016, I-TASSER began using XSEDE’s Comet supercomputer; as a result, I-TASSER singlehandedly tripled Comet’s users by adding more than 8,000 unique users in the first several months of integrating with Comet. In this presentation, we will discuss the following: (1) How I-TASSER generates protein structure and function predictions; (2) how I-TASSER is integrated with the XSEDE Gateway system and how the XSEDE resources have enhanced the functionality of I-TASSER and its usefulness to the community; (3) How to use the I-TASSER Gateway and how to interpret the I-TASSER output results for normal users; and (4) how to improve the quality of the I-TASSER model for advanced users (e.g. introduction of restraints, and strategy for modeling multi-domain proteins etc). The I-TASSER gateway is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER/.

Chem Compute Science Gateway:  Computational Chemistry for Undergraduates
Presented by Mark Perri, Assistant Professor of Chemistry, Sonoma State University

Abstract: We report on our efforts to provide a free, easy to use, but powerful interface for undergraduate students to submit computational jobs.  Computational experiments are critical for engaging students in Physical Chemistry because they provide the opportunity for visualization of concepts, such as molecular orbitals.  The Chem Compute Science Gateway allows students to submit jobs to the NSF XSEDE supercomputer network.  Students can submit jobs using the GAMESS (General Atomic and Molecular Electronic Structure System) ab initio quantum chemistry package and the TINKER Molecular Modeling Package (Molecular Dynamics).

Slides about I-TASSER

Slides about Chem Compute

Watch on YouTube