| An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum. | |
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MedLine Citation:
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PMID: 15951211 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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The understanding of transition processes, such as chemical reactions, is a central topic in theoretical molecular science. A common approach for investigating such processes is to calculate paths between reactant and product structures that are representative of the transition. Many approaches have been proposed to determine such paths but, in this paper, we examine the nudged elastic band algorithm which was recently introduced by Jónsson and co-workers and has been used to study a wide range of transition problems. We describe our implementation of the method in the simulation program Dynamo and some modifications to the original algorithm that we found improve its efficiency. The use of the method is illustrated by an application to the reaction mechanism of the enzyme hypoxanthine-guanine-xanthine phosphoribosyltransferase from Plasmodium falciparum. |
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Authors:
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Ramon Crehuet; Aline Thomas; Martin J Field |
Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2005-06-13 |
Journal Detail:
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Title: Journal of molecular graphics & modelling Volume: 24 ISSN: 1093-3263 ISO Abbreviation: J. Mol. Graph. Model. Publication Date: 2005 Oct |
Date Detail:
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Created Date: 2005-10-03 Completed Date: 2006-01-27 Revised Date: 2006-11-15 |
Medline Journal Info:
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Nlm Unique ID: 9716237 Medline TA: J Mol Graph Model Country: United States |
Other Details:
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Languages: eng Pagination: 102-10 Citation Subset: IM |
Affiliation:
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Institut d'Investigacions Químiques i Ambientals de Barcelona (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain. rcsqtc@iiqab.csic.es |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Alanine
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chemistry Algorithms* Animals Computer Simulation Dipeptides / chemistry Elasticity Models, Molecular* Pentosyltransferases / chemistry*, metabolism Plasmodium falciparum / enzymology* Protozoan Proteins / chemistry*, metabolism Thermodynamics |
| Chemical | |
Reg. No./Substance:
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0/Dipeptides; 0/Protozoan Proteins; 56-41-7/Alanine; EC 2.4.2.-/Pentosyltransferases; EC 2.4.2.-/hypoxanthine-guanine-xanthine phosphoribosyltransferase |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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