FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2417954325> ?p ?o ?g. }

• W2417954325 endingPage "5757" @default.
• W2417954325 startingPage "5747" @default.
• W2417954325 abstract "Molecular dynamics simulations are a powerful means of understanding conformational changes. However, it is still difficult to simulate biologically relevant time scales without the use of specialized supercomputers. Here, we introduce a goal-oriented sampling method, called fluctuation amplification of specific traits (FAST), for extending the capabilities of commodity hardware. This algorithm rapidly searches conformational space for structures with desired properties by balancing trade-offs between focused searches around promising solutions (exploitation) and trying novel solutions (exploration). FAST was inspired by the hypothesis that many physical properties have an overall gradient in conformational space, akin to the energetic gradients that are known to guide proteins to their folded states. For example, we expect that transitioning from a conformation with a small solvent-accessible surface area to one with a large surface area will require passing through a series of conformations with steadily increasing surface areas. We demonstrate that such gradients are common through retrospective analysis of existing Markov state models (MSMs). Then we design the FAST algorithm to exploit these gradients to find structures with desired properties by (1) recognizing and amplifying structural fluctuations along gradients that optimize a selected physical property whenever possible, (2) overcoming barriers that interrupt these overall gradients, and (3) rerouting to discover alternative paths when faced with insurmountable barriers. To test FAST, we compare its performance to other methods for three common types of problems: (1) identifying unexpected binding pockets, (2) discovering the preferred paths between specific structures, and (3) folding proteins. Our conservative estimate is that FAST outperforms conventional simulations and an adaptive sampling algorithm by at least an order of magnitude. Furthermore, FAST yields both the proper thermodynamics and kinetics, allowing for a direct connection with kinetic experiments that is impossible with many other advanced sampling algorithms because they provide only thermodynamic information. Therefore, we expect FAST to be of great utility for a wide range of applications." @default.
• W2417954325 created "2016-06-24" @default.
• W2417954325 creator A5016680758 @default.
• W2417954325 creator A5029297375 @default.
• W2417954325 date "2015-11-20" @default.
• W2417954325 modified "2023-10-13" @default.
• W2417954325 title "FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs" @default.
• W2417954325 cites W1898130445 @default.
• W2417954325 cites W1974225312 @default.
• W2417954325 cites W1976904430 @default.
• W2417954325 cites W1976998887 @default.
• W2417954325 cites W1979070806 @default.
• W2417954325 cites W1984604072 @default.
• W2417954325 cites W1988820633 @default.
• W2417954325 cites W1990593157 @default.
• W2417954325 cites W1992899488 @default.
• W2417954325 cites W2001398410 @default.
• W2417954325 cites W2014095962 @default.
• W2417954325 cites W2016336300 @default.
• W2417954325 cites W2018084703 @default.
• W2417954325 cites W2018657646 @default.
• W2417954325 cites W2021541427 @default.
• W2417954325 cites W2031194866 @default.
• W2417954325 cites W2031843459 @default.
• W2417954325 cites W2040809566 @default.
• W2417954325 cites W2043580883 @default.
• W2417954325 cites W2046285452 @default.
• W2417954325 cites W2049489032 @default.
• W2417954325 cites W2049738344 @default.
• W2417954325 cites W2053348581 @default.
• W2417954325 cites W2055484248 @default.
• W2417954325 cites W2057477511 @default.
• W2417954325 cites W2059013803 @default.
• W2417954325 cites W2060757799 @default.
• W2417954325 cites W2062393760 @default.
• W2417954325 cites W2062421175 @default.
• W2417954325 cites W2066795144 @default.
• W2417954325 cites W2067236515 @default.
• W2417954325 cites W2069620421 @default.
• W2417954325 cites W2073324778 @default.
• W2417954325 cites W2075243501 @default.
• W2417954325 cites W2081645999 @default.
• W2417954325 cites W2085213650 @default.
• W2417954325 cites W2093694964 @default.
• W2417954325 cites W2095213407 @default.
• W2417954325 cites W2098093830 @default.
• W2417954325 cites W2099598754 @default.
• W2417954325 cites W2101348065 @default.
• W2417954325 cites W2111339528 @default.
• W2417954325 cites W2120595908 @default.
• W2417954325 cites W2127737131 @default.
• W2417954325 cites W2142971854 @default.
• W2417954325 cites W2147872249 @default.
• W2417954325 cites W2149655632 @default.
• W2417954325 cites W2155267446 @default.
• W2417954325 cites W2158476854 @default.
• W2417954325 cites W2160544821 @default.
• W2417954325 cites W2164270482 @default.
• W2417954325 cites W2171268876 @default.
• W2417954325 cites W2277366394 @default.
• W2417954325 cites W2313338745 @default.
• W2417954325 cites W2317766861 @default.
• W2417954325 cites W2322017037 @default.
• W2417954325 cites W2322812643 @default.
• W2417954325 cites W2543580944 @default.
• W2417954325 cites W2949836140 @default.
• W2417954325 cites W2951093718 @default.
• W2417954325 cites W3047967427 @default.
• W2417954325 cites W3101066868 @default.
• W2417954325 cites W4245744705 @default.
• W2417954325 cites W4246270964 @default.
• W2417954325 cites W4254234218 @default.
• W2417954325 cites W585413800 @default.
• W2417954325 doi "https://doi.org/10.1021/acs.jctc.5b00737" @default.
• W2417954325 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26588361" @default.
• W2417954325 hasPublicationYear "2015" @default.
• W2417954325 type Work @default.
• W2417954325 sameAs 2417954325 @default.
• W2417954325 citedByCount "128" @default.
• W2417954325 countsByYear W24179543252016 @default.
• W2417954325 countsByYear W24179543252017 @default.
• W2417954325 countsByYear W24179543252018 @default.
• W2417954325 countsByYear W24179543252019 @default.
• W2417954325 countsByYear W24179543252020 @default.
• W2417954325 countsByYear W24179543252021 @default.
• W2417954325 countsByYear W24179543252022 @default.
• W2417954325 countsByYear W24179543252023 @default.
• W2417954325 crossrefType "journal-article" @default.
• W2417954325 hasAuthorship W2417954325A5016680758 @default.
• W2417954325 hasAuthorship W2417954325A5029297375 @default.
• W2417954325 hasConcept C111919701 @default.
• W2417954325 hasConcept C11413529 @default.
• W2417954325 hasConcept C119599485 @default.
• W2417954325 hasConcept C119857082 @default.
• W2417954325 hasConcept C127413603 @default.
• W2417954325 hasConcept C147597530 @default.
• W2417954325 hasConcept C165696696 @default.
• W2417954325 hasConcept C185592680 @default.

• next