Lafire: a software for automatic protein structure refinement
نویسندگان
چکیده
منابع مشابه
An integrated software environment for protein structure refinement
The development of an integrated software environment for protein structure refinement is reported. Energy minimization is combined with geometric embedding in the refinement program. The energy minimization procedure is used to sample the conformational space and find a group of low energy structures for further improvement. The distance geometry also known as geometric embedding is then appli...
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This thesis presents various techniques that aim at enabling more effective and more efficient approaches for automatic software verification. After a brief motivation why automatic software verification is getting ever more relevant, we continue with detailing the formalism used in this thesis and on the concepts it is built on. We then describe the design and implementation of the value analy...
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Refining an initial protein model to its final structure is usually composed of rounds of refinement performed by programs such as CNS and REFMAC, and manual model modification that includes linking and extending fragments, and fitting the ill matched residues of model by using the computer graphics program such as O. The manual model modification requires expertise of crystallography to recogn...
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Knowledge-based protein potentials are simplified potentials designed to improve the quality of protein models, which is important as more accurate models are more useful for biological and pharmaceutical studies. Consequently, knowledge-based potentials often are designed to be efficient in ordering a given set of deformed structures denoted decoys according to how close they are to the releva...
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Conditional optimization allows unlabelled loose-atom refinement to be combined with extensive application of geometrical restraints. It offers an N-particle solution for the assignment of topology to loose atoms, with weighted gradients applied to all possibilities. For a simplified test structure consisting of a polyalanine four-helical bundle, this method shows a large radius of convergence ...
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ژورنال
عنوان ژورنال: Acta Crystallographica Section A Foundations of Crystallography
سال: 2005
ISSN: 0108-7673
DOI: 10.1107/s0108767305093098