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Protocols

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PRODRG specifications

Information


Unique identifier OMICS_04955
Name PRODRG
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PRODRG

PRODRG in pipelines

 (8)
2017
PMCID: 5493083
PMID: 28666484
DOI: 10.1186/s40199-017-0182-0

[…] was carried out with the gromacs 5.0.5 package []. the topology parameters of the best predicted ligand in terms of the energy and interaction between ligand and protein were created by the prodrg web server []. the generated charges by this server were corrected by gaussian98 program. the pka for residues of protein were obtained by the propka 3.1 web server to determined which residue […]

2016
PMCID: 4904370
PMID: 27292548
DOI: 10.1038/srep27128

[…] square (rms) cut-off of 3 å. the cluster with highest affinity was selected as the preferable binding mode. for molecular dynamics (md), the structures of dopc and dppc were parameterized using the prodrg server. the gromacs package (version 4.5) was used for performing the md simulations. the structures in complex with, or without, lipid were immersed in a cubic water box, with a distance […]

2016
PMCID: 4911049
PMID: 27311013
DOI: 10.1371/journal.pone.0157286

[…] were collected at every 500 ps. production run at each temperature was replicated using different seed numbers for tdt-short and tdt-long isoforms. parameters of substrate (ddatp) were obtained from prodrg server []., loop3 (twenty residue insert) is positioned on the surface of tdt and possess charged residues, especially four lysines (lys 484, lys 494, lys 496, lys 500), which may […]

2016
PMCID: 4942797
PMID: 27405411
DOI: 10.1038/srep29511

[…] using the web-based graphical user interface for charmm (http://www.charmm-gui.org) and then equilibrated with gromacs. the topology and parameters files for the dmpc molecule were generated by prodrg (http://davapc1.bioch.dundee.ac.uk/prodrg/). the limit on lipid molecules allowed in haddock simulations was raised in order to implement bilayers in the docking calculations (i.e., maxtree […]

2016
PMCID: 5239439
PMID: 27384997
DOI: 10.18632/oncotarget.10341

[…] and its inhibitors. we used gromacs 4.5 [] for linux for molecular dynamics simulation., the topology file, partial charges and force field parameters for ligand atoms were generated by the dundee prodrg 2.5 server (university of dundee, dundee, scotland) (beta) []. taking ptp-meg2 as an example, the simulation system was solvated in a specific box with spc water solute [, ] and sodium […]


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PRODRG in publications

 (372)
PMCID: 5913338
PMID: 29686295
DOI: 10.1038/s41598-018-23840-2

[…] a docking model of curcumin binding to stat3 protein. the structures of stat3 are from protein data bank (pdb id: 3cwg and pdb id: 1bg1). curcumin coordinates were obtained from the glycobiochem prodrg2 server (http://davapc1.bioch.dundee.ac.uk/prodrg/). the grid maps for the docking model was set to have 74 × 126 × 126 points with 1.0 å spacing to cover all surface of stat3. […]

PMCID: 5905284
PMID: 29719578
DOI: 10.3762/bjoc.14.69

[…] [] giving a final r 1 index of ≈0.10. due to the structural complexity of the inclusion compound, soft restraints on bond lengths and angles of the host and guest molecules were applied using the prodrg2 webserver [] and along with dfix, dang and flat commands in shelxl. h-atoms of β-cd and cholesterol molecules were placed geometrically for temperature of 100 k and allowed to ride […]

PMCID: 5953856
DOI: 10.6026/97320630014101

[…] used for screening a local database containing 1,000,000 lead like small molecules., gromacs md package 4.6.5 [] was used to simulate the toxt-ligand(s) interactions in a dynamic environment. the prodrg server that is based on the gromos force field was employed to generate topology files for ligands []. gromos96 force field with a modified version of the 53a6.ff force field was utilized […]

PMCID: 5883087
PMID: 29644215
DOI: 10.3389/fchem.2018.00091

[…] both exo and endo conformations of the pyrrolidine ring., structure calculation and refinement was performed using cns software (brunger et al., ). topology and parameter files were prepared using a prodrg server (schuttelkopf and van aalten, ) and manually checked and corrected. the refinement protocol included a high-temperature cartesian molecular dynamic phase (15 ps at t = 50,000 k) […]

PMCID: 5870988
PMID: 29584771
DOI: 10.1371/journal.pone.0194934

[…] human αβ-tubulin isotypes with indanocine, molecular docking was performed using autodock4.2 []. for molecular docking, energy-minimized 3d atomic coordinates of indanocine were generated using the prodrg server []. since indanocine was suggested to bind at the interface of αβ tubulin [], an autogrid was used to outline the putative binding pocket around the interface of αβ tubulin []. […]


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PRODRG institution(s)
Department of Biochemistry and Molecular Biology, University of Leeds, UK

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