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NMSim specifications

Information


Unique identifier OMICS_07560
Name NMSim
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Publications for NMSim

NMSim in publications

 (14)
PMCID: 5714956
PMID: 29203888
DOI: 10.1038/s41598-017-17088-5

[…] ensemble of the free stat6 in order to describe the conformational space sampled by the peptide in the absence of the binding partner more comprehensively. the normal mode-based simulation (nmsim) approach has been shown to be a computationally efficient alternative to molecular dynamics simulation for conformational sampling of proteins. therefore, starting from the nmr structure […]

PMCID: 5670125
PMID: 29101342
DOI: 10.1038/s41598-017-15075-4

[…] of monomer a from wt (1nns) and monomer b from n24s (5mq5) in complex with the l-aspartate product, and hence in the more compact conformation, were used for normal mode-based geometric simulations (nmsim). loop motion was analyzed by small scale motions, whole protein motions were analyzed both with the lowest and largest radius of gyration (rog) using default parameters […]

PMCID: 5636086
PMID: 29020017
DOI: 10.1371/journal.pone.0185658

[…] to minimize their conformational energy in order to predict the transition pathway successfully []. such nma-based transition pathway prediction tools were also addressed through online web servers. nmsim reproduces the feasible transition pathways using rigid-cluster nma in cartesian coordinates [], while imods performs the pathway generation based on nma in internal coordinates []., […]

PMCID: 5556012
PMID: 28808308
DOI: 10.1038/s41598-017-08521-w

[…] or e) atp-bound. state c) resembles what has been found in pdb id 5jvj. intermediate states between the open and closed nbd conformations of chain a were generated by targeted simulations with the nmsim approach, , as done before. the umbrella windows display considerable overlap regarding the frequency distribution of values for the reaction coordinate (supplementary fig. ). furthermore, […]

PMCID: 5371819
PMID: 28358005
DOI: 10.1038/srep45389

[…] for the potential of mean force calculations, plausible pathways of the swiveling motion and opening-closing motion have been generated using targeted normal mode-based geometric simulations by the nmsim approach. nmsim is a three-step protocol for multiscale modeling of protein conformational changes that incorporates information about preferred directions of protein motions into a geometric […]


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NMSim institution(s)
Computational Pharmaceutical Chemistry Group, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Düsseldorf, Germany

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