نتایج جستجو برای: rosetta
تعداد نتایج: 1746 فیلتر نتایج به سال:
Parallel Tempering (PT) is an effective algorithm to overcome the slow convergence in low-temperature protein simulation by initiating multiple systems to run at multiple temperature levels and randomly switch with neighbor temperature levels. We implemented the PT scheme in the Rosetta to explore the rough energy landscape in protein folding and to improve the success rate of Rosetta in topolo...
We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained ...
The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a...
Motivation The identification of T-cell epitopes has many profound translational applications in the areas of transplantation, disease diagnosis, vaccine/therapeutic protein development and personalized immunotherapy. While data-driven methods have been widely used for the prediction of peptide binders with notable successes, the structural modeling of peptide binding to MHC molecules is crucia...
Summary Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific...
A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents Rosetta results for four well-defined test cases: the...
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to appro...
Rosetta is a European Space Agency (ESA) cornerstone mission that entered orbit around the comet 67P/Churyumov-Gerasimenko in August 2014 and will escort the comet for a 1.5 year nominal mission offering the most detailed study of a comet ever undertaken by humankind. The Rosetta orbiter has 11 scientific instruments (4 remote sensing) and the Philae lander to make complementary measurements of...
The Rosetta systems level design language [1, 2] is an emerging standard designed to address the integration of information across domains. Specifically, Rosetta directly supports specifying and integrating models whose basic computation models differ due to technology domain. Rosetta achieves this by providing a framework where models of computation and domain specific information can be defin...
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