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Protocols

ANMPathway specifications

Information


Unique identifier OMICS_14348
Name ANMPathway
Alternative name Anisotropic Network Model Pathway
Interface Web user interface
Restrictions to use None
Input data A protein structure
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline ANMPathway

Publication for Anisotropic Network Model Pathway

ANMPathway citations

 (8)
library_books

Normal mode guided transition pathway generation in proteins

2017
PLoS One
PMCID: 5636086
PMID: 29020017
DOI: 10.1371/journal.pone.0185658

[…] ount any physical aspects such as the intrinsic thermal vibration, but only complies with the given topological constraints in Cartesian space. As the existing morphing methods such as MENM, iENM and ANMPathway also utilize either topological constraints or potential energy landscape for prediction of large-scale transition pathways, our method is expected to be a new solution considering both asp […]

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Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data

2017
PMCID: 5315668
PMID: 28289692
DOI: 10.1063/1.4976142
call_split See protocol

[…] atoms in the PATH trajectory remained within the range of experimentally observed values. We provided more convincing validation by comparing the PATH results with other computational algorithms like ANMPathway, using Replica Exchange Discrete Molecular Dynamics simulations to map the free energy surfaces linking the two ground states, and showing that PATH identified the transition state close to […]

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Revisiting the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective

2016
Sci Rep
PMCID: 4958977
PMID: 27453290
DOI: 10.1038/srep30105
call_split See protocol

[…] ally (high Ca2+ concentration) activated FXIIIAa crystal structure (PDB ID: 4kty; 1.8 Å resolution). The intermediates were generated by submitting these two structures as end-state structures to the ANMPathway server (http://anmpathway.lcrc.anl.gov/anmpathway.cgi; accessed on 08.11.2014), which uses a coarse-grained modeling approach to construct a two-state potential calculated by combining two […]

library_books

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

2016
PLoS Comput Biol
PMCID: 4849799
PMID: 27124275
DOI: 10.1371/journal.pcbi.1004619

[…] llectively along the modes predicted by the ANM. A Metropolis-based MC scheme is employed to select the ANM modes; the stochasticity permits the system to occasionally circumvent energy barriers. The ANMPathway is a related sampling method that uses modes extracted from two ENMs representative of the experimental structures that constitute the end points of the transition under investigation []. B […]

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A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

2016
PMCID: 4769271
PMID: 26958584
DOI: 10.1063/1.4941599
call_split See protocol

[…] We compared trajectories from the simulations of the converter domain from myosin VI performed using the string method, ANMPathway, and PATH. Since the reaction coordinates of the three trajectories are different, it would be difficult to compare them at every instant. We compare in Fig. the structural similarity and […]

library_books

The selectivity of the Na+/K+ pump is controlled by binding site protonation and self correcting occlusion

2016
eLife
PMCID: 5026471
PMID: 27490484
DOI: 10.7554/eLife.16616.017

[…] econd connects states E2(K2) and K2·E1, and the third describes the transition between states Na3·E1-P and P-E2·Na3. First, A Cα-atom-only transition pathway for each of these was generated using the ANMPathway online server (http://anmpathway.lcrc.anl.gov/anmpathway.cgi) () based on the SERCA pump crystal structures including 3B9B (), 1WPG (), and 1VFP (). Since both the Na+/K+-pump and the Ca2+ […]

Citations

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ANMPathway institution(s)
Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, IL, USA; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
ANMPathway funding source(s)
This work was funded by grant U54-GM087519 from the National Institute of Health (NIH).

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