نتایج جستجو برای: rosetta
تعداد نتایج: 1746 فیلتر نتایج به سال:
Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for...
The predictive modeling and design of biologically active RNA molecules requires understanding the energetic balance among their basic components. Rapid developments in computer simulation promise increasingly accurate recovery of RNA's nearest-neighbor (NN) free-energy parameters, but these methods have not been tested in predictive trials or on nonstandard nucleotides. Here, we present, to ou...
NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assig...
Rosetta is one of the prime tools for high resolution protein structure refinement. While its scoring function can distinguish native-like from non-native-like conformations in many cases, the method is limited by conformational sampling for larger proteins, that is, leaving a local energy minimum in which the search algorithm may get stuck. Here, we test the hypothesis that iteration of Rosett...
This report outlines an approach to use rough set theory and the ROSETTA system in the field of fault diagnosis in rotating machinery. The complexity of rotating machinery makes fault diagnosis a difficult task. Several computer based methods exist using mathematical modelling together with fuzzy logic, neural networks, faults matrices, machine specific experience and simulation. The ROSETTA sy...
SUMMARY PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating ene...
This paper discusses the translation of temporal expressions, in the framework of the machine translation system Rosetta. The translation method of Rosetta, the "isomorphic grammar method', is based on Montague's Compositionality Principle. It is shown that a compositional approach leads to a transparent account of the complex aspects of time in natural language and can be used for the translat...
Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and guiding their improvement, and illustrate the application of these tools to the improvement of the Rosetta energy function. The feature analysis tool identifies discrepancies between structures deposited in the PDB and low-energy structures gen...
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