Abstract：
:Functional conformational changes of proteins can facilitate numerous biological events in cells. The Markov state model (MSM) built from molecular dynamics simulations provide a powerful approach to study them. We here introduce a protocol that is tailor-made for constructing MSMs to study the functional conformational changes of proteins. In this protocol, one of the important steps is to select proper molecular features that can collectively describe the slowest timescales of conformational changes of interest. We recommend spectral oASIS, the modified version of oASIS, as a promising approach for automatic feature selection. Recently developed deep learning methods could also serve efficient approaches for selecting features and finding collective variables. Using DNA repair enzymes and RNA polymerases as examples, we review recent applications of MSMs to elucidate molecular mechanisms of functional conformational changes. Finally, we discuss remaining challenges and future perspectives for constructing MSMs to study functional conformational changes of proteins.
journal_name
Curr Opin Struct Bioljournal_title
Current opinion in structural biologyauthors
Wang X,Unarta IC,Cheung PP,Huang Xdoi
10.1016/j.sbi.2020.10.005subject
Has Abstractpub_date
2020-10-27 00:00:00pages
69-77eissn
0959-440Xissn
1879-033Xpii
S0959-440X(20)30172-Xjournal_volume
67pub_type
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
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journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
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更新日期：2018-04-01 00:00:00
