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1.
Enhanced
sampling
simulations to construct free-energy landscape of protein–partner substrate interaction
作者:
Jinzen Ikebe
;
Koji Umezawa
;
Junichi Higo
关键词:
Molecular dynamics simulation
;
Enhanced
sampling
;
Multicanonical
;
Conformational
ensemble
;
Protein interaction
刊名:Biophysical Reviews
出版者:Springer Berlin / Heidelberg
年:2016
2.
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations
作者:
Dominik Buddaya
;
dominik.budday@fau.de" class="auth_mail" title="E-mail the corresponding author
;
Sigrid Leyendeckera
;
sigrid.leyendecker@ltd.uni-erlangen.de" class="auth_mail" title="E-mail the corresponding author
;
Henry van den Bedemb
;
vdbedem@stanford.edu" class="auth_mail" title="E-mail the corresponding author
关键词:
Protein
;
Rigidity
;
Nullspace
;
Singular configuration
;
Protein collective motions
;
Conformational
sampling
刊名:Journal of the Mechanics and Physics of Solids
年:2015
3.
Native structure-based modeling and simulation of biomolecular systems per mouse click
作者:
Benjamin Lutz
;
Claude Sinner
;
Stefan Bozic
;
Ivan Kondov…
关键词:
Protein folding
;
RNA folding
;
Native structure
;
based model
;
Molecular dynamics
;
GridBeans
刊名:BMC Bioinformatics
出版者:BioMed Central
年:2014
4.
Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics
作者:
Ya-Wen Hsiao (1) P?r S?derhjelm (2)
关键词:
Funnel metadynamics
;
Binding affinity
;
CGENFF
;
GAFF
;
NAMD
刊名:Journal of Computer-Aided Molecular Design
年:2014
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