Zobrazeno 1 - 10
of 21
pro vyhledávání: '"Robert K.-Z. Tan"'
Publikováno v:
Journal of Structural Biology. 163:163-174
The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::be307c57b1fe90254698527abbe871d2
https://doi.org/10.1016/j.jsb.2008.05.001
https://doi.org/10.1016/j.jsb.2008.05.001
Publikováno v:
Journal of Chemical Theory and Computation. 2:529-540
Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to m
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f90cb7278dd4bdecd293223040f1a563
https://doi.org/10.1021/ct050323r
https://doi.org/10.1021/ct050323r
Publikováno v:
Multiscale Modeling & Simulation. 5:1248-1263
Low-resolution molecular models can provide appropriate and efficient ways for studying large biomolecular systems such as the ribosome. We have developed computer codes that use the Yammp Under Python modeling package to assemble low-resolution forc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::24f130fa1306a7f1c0fbb5bdf1424d4e
https://doi.org/10.1137/05064850x
https://doi.org/10.1137/05064850x
Publikováno v:
Biopolymers. 39:259-278
Small (600 base pair) DNA plasmids were modeled with a simplified representation (3DNA) and the intramolecular motions were studied using molecular mechanics and molecular dynamics techniques. The model is detailed enough to incorporate sequence effe
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::98ea3765fd53859b3b2ba23892235340
https://doi.org/10.1002/(sici)1097-0282(199608)39:2<259::aid-bip12>3.0.co
https://doi.org/10.1002/(sici)1097-0282(199608)39:2<259::aid-bip12>3.0.co
Publikováno v:
Biopolymers. 39:243-258
Many modeling studies of supercoiled DNA are based on equilibrium structures from theoretical calculations or energy minimization. Since closed circular DNAs are flexible, it is possible that errors are introduced by calculating properties from a sin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::692d72fd80ece39bcbd8ebeb5d3e511b
https://doi.org/10.1002/(sici)1097-0282(199608)39:2<243::aid-bip11>3.0.co
https://doi.org/10.1002/(sici)1097-0282(199608)39:2<243::aid-bip11>3.0.co
Publikováno v:
Journal of Computational Chemistry. 19:726-740
This article describes an unexpected phenomenon encountered during MD simulations: velocity rescaling using standard protocols can systematically change the proportion of total kinetic energy (KE) found in motions associated with the various degrees
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::555fd03623dd0683c9e0b1a2f6352b1a
https://doi.org/10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co
https://doi.org/10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co
Publikováno v:
Scopus-Elsevier
We have analyzed the reactivity of a 217 base pair segment of the intrinsically curved Crithidia fasciculata kinetoplast DNA towards eukaryotic DNA topoisomerase I. The substrates were open [linear fragment and nicked circle] and closed minidomains [
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::112b6c4ce842049e1ac4ec1c69441fae
https://doi.org/10.1080/07391102.1996.10508897
https://doi.org/10.1080/07391102.1996.10508897
Publikováno v:
Molecular Engineering. 5:213-218
In the absence of a high resolution crystal structure for the ribosome, numerous research groups are carrying out low resolution structural studies using neutron diffraction, electron microscopy, fluorescence energy transfer, chemical crosslinking, c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7100dba2fd64abc190e2b8b42507b990
https://doi.org/10.1007/bf00999589
https://doi.org/10.1007/bf00999589
Publikováno v:
Biophysical Journal. 66:1777-1795
There is a growing body of low-resolution structural data that can be utilized to devise structural models for large RNAs and ribonucleoproteins. These models are routinely built manually. We introduce an automated refinement protocol to utilize such
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d5ee2f27ef53442176643a1cd7b443c4
https://doi.org/10.1016/s0006-3495(94)80972-5
https://doi.org/10.1016/s0006-3495(94)80972-5
Publikováno v:
Journal of Computational Chemistry. 15:190-199
This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron-microscopy–based three-dimensional image reconstruction f
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ab18b06b770bb33472d1d05adf25ceac
https://doi.org/10.1002/jcc.540150209
https://doi.org/10.1002/jcc.540150209