FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3100486827> ?p ?o ?g. }

• W3100486827 abstract "Abstract Markov state models (MSMs) have been widely applied to study the kinetics and pathways of protein conformational dynamics based on statistical analysis of molecular dynamics (MD) simulations. These MSMs coarse-grain both configuration space and time in ways that limit what kinds of observables they can reproduce with high fidelity over different spatial and temporal resolutions. Despite their popularity, there is still limited understanding of which biophysical observables can be computed from these MSMs in a robust and unbiased manner, and which suffer from the space-time coarse-graining intrinsic in the MSM model. Most theoretical arguments and practical validity tests for MSMs rely on long-time equilibrium kinetics, such as the slowest relaxation timescales and experimentally observable time-correlation functions. Here, we perform an extensive assessment of the ability of well-validated protein folding MSMs to accuractely reproduce path-based observable such as mean first-passage times (MFPTs) and transition path mechanisms compared to a direct trajectory analysis. We also assess a recently proposed class of history-augmented MSMs (haMSMs) that exploit additional information not accounted for in standard MSMs. We conclude with some practical guidance on the use of MSMs to study various problems in conformational dynamics of biomolecules. In brief, MSMs can accurately reproduce correlation functions slower than the lag time, but path-based observables can only be reliably reproduced if the lifetimes of states exceed the lag time, which is a much stricter requirement. Even in the presence of short-lived states, we find that haMSMs reproduce path-based observables more reliably." @default.
• W3100486827 created "2020-11-23" @default.
• W3100486827 creator A5003813944 @default.
• W3100486827 creator A5012092373 @default.
• W3100486827 creator A5013886149 @default.
• W3100486827 creator A5055016850 @default.
• W3100486827 creator A5083925073 @default.
• W3100486827 creator A5090875333 @default.
• W3100486827 date "2020-11-09" @default.
• W3100486827 modified "2023-09-25" @default.
• W3100486827 title "What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models" @default.
• W3100486827 cites W1031578623 @default.
• W3100486827 cites W1482044830 @default.
• W3100486827 cites W1542407515 @default.
• W3100486827 cites W1575877217 @default.
• W3100486827 cites W165538626 @default.
• W3100486827 cites W1809666471 @default.
• W3100486827 cites W1977875643 @default.
• W3100486827 cites W1987887771 @default.
• W3100486827 cites W1988220126 @default.
• W3100486827 cites W1989544083 @default.
• W3100486827 cites W1991901383 @default.
• W3100486827 cites W1995748690 @default.
• W3100486827 cites W1996821584 @default.
• W3100486827 cites W2001398410 @default.
• W3100486827 cites W2001548057 @default.
• W3100486827 cites W2016336300 @default.
• W3100486827 cites W2022231452 @default.
• W3100486827 cites W2022702839 @default.
• W3100486827 cites W2025899185 @default.
• W3100486827 cites W2026134081 @default.
• W3100486827 cites W2027593773 @default.
• W3100486827 cites W2029667189 @default.
• W3100486827 cites W2033238191 @default.
• W3100486827 cites W2044201287 @default.
• W3100486827 cites W2053348581 @default.
• W3100486827 cites W2060302048 @default.
• W3100486827 cites W2063021109 @default.
• W3100486827 cites W2064556178 @default.
• W3100486827 cites W2065281489 @default.
• W3100486827 cites W2065963893 @default.
• W3100486827 cites W2067236515 @default.
• W3100486827 cites W2068540815 @default.
• W3100486827 cites W2075243501 @default.
• W3100486827 cites W2080076400 @default.
• W3100486827 cites W2080454718 @default.
• W3100486827 cites W2082586732 @default.
• W3100486827 cites W2085213650 @default.
• W3100486827 cites W2087631644 @default.
• W3100486827 cites W2091510866 @default.
• W3100486827 cites W2091983181 @default.
• W3100486827 cites W2110507597 @default.
• W3100486827 cites W2111339528 @default.
• W3100486827 cites W2122638517 @default.
• W3100486827 cites W2152385114 @default.
• W3100486827 cites W2157019488 @default.
• W3100486827 cites W2160341881 @default.
• W3100486827 cites W2165249142 @default.
• W3100486827 cites W2226825552 @default.
• W3100486827 cites W2313116527 @default.
• W3100486827 cites W2315297180 @default.
• W3100486827 cites W2469262244 @default.
• W3100486827 cites W2510365122 @default.
• W3100486827 cites W2528583500 @default.
• W3100486827 cites W2532617145 @default.
• W3100486827 cites W2554489021 @default.
• W3100486827 cites W2570547882 @default.
• W3100486827 cites W2577671591 @default.
• W3100486827 cites W2764032733 @default.
• W3100486827 cites W2783073729 @default.
• W3100486827 cites W2922136662 @default.
• W3100486827 cites W2947171186 @default.
• W3100486827 cites W2949223833 @default.
• W3100486827 cites W2951478780 @default.
• W3100486827 cites W2964149432 @default.
• W3100486827 cites W2995307719 @default.
• W3100486827 cites W3047967427 @default.
• W3100486827 cites W3100276353 @default.
• W3100486827 cites W3100810942 @default.
• W3100486827 cites W3102325889 @default.
• W3100486827 cites W3105487324 @default.
• W3100486827 cites W3106252157 @default.
• W3100486827 cites W3106467705 @default.
• W3100486827 cites W4213311833 @default.
• W3100486827 cites W4251218076 @default.
• W3100486827 doi "https://doi.org/10.1101/2020.11.09.374496" @default.
• W3100486827 hasPublicationYear "2020" @default.
• W3100486827 type Work @default.
• W3100486827 sameAs 3100486827 @default.
• W3100486827 citedByCount "3" @default.
• W3100486827 countsByYear W31004868272021 @default.
• W3100486827 countsByYear W31004868272022 @default.
• W3100486827 crossrefType "posted-content" @default.
• W3100486827 hasAuthorship W3100486827A5003813944 @default.
• W3100486827 hasAuthorship W3100486827A5012092373 @default.
• W3100486827 hasAuthorship W3100486827A5013886149 @default.
• W3100486827 hasAuthorship W3100486827A5055016850 @default.
• W3100486827 hasAuthorship W3100486827A5083925073 @default.
• W3100486827 hasAuthorship W3100486827A5090875333 @default.
• W3100486827 hasBestOaLocation W31004868271 @default.

• next