2019
DOI: 10.1002/jcc.26083
|View full text |Cite
|
Sign up to set email alerts
|

FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules

Abstract: Reliable conformational sampling and trajectory analysis are always important to the study of the folding or binding mechanisms of biomolecules. Generally, one has to prepare many complicated parameters and follow a lot of steps to obtain the final data. The whole process is too complicated to new users. In this article, we provide a convenient and user‐friendly tool that is compatible to AMBER, called fast sampling and analysis tool (FSATOOL). FSATOOL has some useful features. First and the most important, th… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

0
19
0

Year Published

2020
2020
2024
2024

Publication Types

Select...
5

Relationship

4
1

Authors

Journals

citations
Cited by 6 publications
(19 citation statements)
references
References 83 publications
(156 reference statements)
0
19
0
Order By: Relevance
“…It is capable of constructing a transition network for microstates or macrostates from lots of short trajectories and presenting the long‐term dynamics of the protein 18,74,75,78 . The work is done by the MSM module in FSATOOL 82 . It first clusters all the snapshots into 48 macrostates.…”
Section: Resultsmentioning
confidence: 99%
See 2 more Smart Citations
“…It is capable of constructing a transition network for microstates or macrostates from lots of short trajectories and presenting the long‐term dynamics of the protein 18,74,75,78 . The work is done by the MSM module in FSATOOL 82 . It first clusters all the snapshots into 48 macrostates.…”
Section: Resultsmentioning
confidence: 99%
“…Recently, we released a software tool for the mixing REMD simulation, called FSATOOL 82 . It has an interface to AMBER18 83 .…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Regular MD shows the structural stability of the k-turn in a free or protein-bound state. And mixing REMD (24,25) (discussed in the next section) provides the widely distributed sampling data for the study of the state transitions.…”
Section: Simulation Protocolsmentioning
confidence: 99%
“…Mixing REMD is an efficient simulation method for biomolecules (24,25). It combines the advantages of the biased and unbiased sampling strategies.…”
Section: Mixing Remd Simulationmentioning
confidence: 99%