Computational {studies|research} of {large|big|huge|massive|substantial|significant} molecular systems are {often|frequently|usually|typically|generally|normally} hindered by resource constraints, {such as|like|including|for example|for instance|which include} the {available|accessible|obtainable|offered|readily available|out there} computational time. A {common|typical|frequent|widespread|prevalent|popular} {approach|method|strategy} to {reduce|decrease|minimize|lessen|lower|cut down} the computational {cost|price|expense} {is to|would be to|is always to|is usually to|will be to|should be to} use a coarse-grained description {instead of|rather than|as opposed to|as an alternative to|in place of} an all-atom representation. {However|Nevertheless|Nonetheless|Even so|On the other hand|Having said that}, such a simpli cation {requires|demands|needs|calls for} {careful|cautious} consideration {of the|from the|in the|on the|with the|of your} coarse-graining scheme to {identify|determine|recognize} {potential|possible|prospective} artefacts introduced {and the|and also the|as well as the|along with the|plus the} limitations {of the|from the|in the|on the|with the|of your} model. {In this|Within this} contribution, we {use the|make use of the} computational {energy|power} landscape framework to explicitly {explore|discover} the {energy|power} landscapes {for a|to get a|for any} coarse-grained (HiRE-RNA) and an all-atom {potential|possible|prospective} (AMBER) for an {example|instance} {system|method|program|technique}, the Aquifex aeolicus tmRNApseudoknot PK1. The {method|technique|approach|strategy|system|process} {provides|offers|gives|supplies|delivers} insight into structural, thermodynamic and kinetic properties {within|inside} a {common|typical|frequent|widespread|prevalent|popular} framework, and {allows|enables|permits|makes it possible for} {for a|to get a|for any} comparison of {a variety of|a number of|many different|various|a range of|several different} {commonly|generally|typically|frequently|normally|usually} computed observables, demonstrating the usefulness of this {approach|method|strategy}.For the speci c case study, we observe that {both|each} potentials exhibit {a number of|numerous|several|quite a few|a variety of|many} {common|typical|frequent|widespread|prevalent|popular} {features|attributes|functions|characteristics|capabilities|options}, highlighting that the coarse-grained model captures {essential|important|crucial|vital|necessary|critical} physical {features|attributes|functions|characteristics|capabilities|options} {of the|from the|in the|on the|with the|of your} {system|method|program|technique}. Nonetheless, we observe shortcomings, and we demonstrate how our {approach|method|strategy} {allows|enables|permits|makes it possible for} us {to improve|to enhance} the model {based on|according to|depending on|determined by} the insight obtained {from the|in the} computational modelling. 882670-92-0 structure 4-Bromo-3-methoxypyridine hydrochloride Chemscene PMID:23618405
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