ProDy protocols

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ProDy specifications

Information


Unique identifier OMICS_07566
Name ProDy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for ProDy

ProDy in pipelines

 (2)
2016
PMCID: 4892583
PMID: 27258022
DOI: 10.1371/journal.pone.0157162

[…] analysis was also applied to x-ray-solved structures of impα complexed with different types of bipartite nlss. these structures were retrieved by the basic local alignment search tool allocated at prody software [] using the impα -nplnls model as the query. only structures with 100% of sequence identity to impα were selected to be compared to the simulation data., the initial comparison […]

2013
PMCID: 3868957
PMID: 24356467
DOI: 10.1038/srep03566

[…] and the simulation of apo-ribu is performed for 180 nanoseconds. rmsf analysis is performed with gromacs employing the g_rmsf module. principle component analysis (pca) is performed through the prody interface of the normal mode wizards module in vmd., in the molecular mechanics poisson-boltzmann (mm-pb) analysis, enthalpy of protein-ligand binding could be decomposed into and evaluated as, […]


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ProDy in publications

 (55)
PMCID: 5941172
PMID: 29735731
DOI: 10.1098/rstb.2017.0177

[…] functional significance of oligomeric states and binding of accessory substrates or lipids that may further modulate their allosteric cooperativity among the protomers., we used several modules in prody [] for performing various tasks, including structural alignments, pca and anm analyses, and comparisons with experimental deformations. details are provided in the electronic supplementary […]

PMCID: 5912754
PMID: 29684031
DOI: 10.1371/journal.pone.0195980

[…] and then allowed to equilibrate for 1 ns in the npt ensemble. finally, a 100ns production trajectory was obtained. structures of the protein along the md trajectory were parsed for every 50 ps using prody v1.2 [], generating a total of 6000 structures. pairwise average linkage hierarchical clustering rmsd clustering was used to cluster these structures with maxcluster [] using the rmsd distance […]

PMCID: 5910821
PMID: 29610305
DOI: 10.1073/pnas.1715896115

[…] robust methods. to this aim, we evaluated a set of features uniquely defined by 3d topology, generated by elastic network models (enms) for proteins (), using the application programming interface prody (). earlier work demonstrated the relevance of enm-predicted motions to biomolecular mechanisms of function and interactions (, )., prody outputs include the identity of sites implicated […]

PMCID: 5854381
PMID: 29543870
DOI: 10.1371/journal.pone.0194425

[…] that 0.1 kcal/mol. the decoy with the lowest total energy was saved as the scabin·nad+·dna ternary complex model., all the structure dynamics calculations were performed in the protein dynamics (prody) package release 1.5.1 [] using python 2.7.9 (python software foundation, delaware, usa). the normal mode wizard (nmwiz) release 1.2 was plugged into the visual molecular dynamics (vmd) viewer, […]

PMCID: 5849682
PMID: 29535344
DOI: 10.1038/s41598-018-22747-2

[…] interaction we also adopted the particle mesh ewald scheme. the dynamic cross-correlation coefficients for c-alpha atoms was calculated on 1000 snapshots extracted from 100 ns md trajectories using prody software. the matrix of all inter-atomic cross-correlations of atomic fluctuations cij where i and j are c-alpha atoms, can be represented as a dynamical cross-correlation map. […]


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