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Protocols

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 citations

 (444)
library_books

Curcumin interacts directly with the Cysteine 259 residue of STAT3 and induces apoptosis in H Ras transformed human mammary epithelial cells

2018
Sci Rep
PMCID: 5913338
PMID: 29686295
DOI: 10.1038/s41598-018-23840-2

[…] make 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. Other parameters […]

library_books

Crystal structure of the inclusion complex of cholesterol in β cyclodextrin and molecular dynamics studies

2018
Beilstein J Org Chem
PMCID: 5905284
PMID: 29719578
DOI: 10.3762/bjoc.14.69

[…] GUI [] 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 on the pare […]

call_split

Glucose regulated protein 78 substrate binding domain alters its conformation upon EGCG inhibitor binding to nucleotide binding domain: Molecular dynamics studies

2018
Sci Rep
PMCID: 5882873
PMID: 29615633
DOI: 10.1038/s41598-018-22905-6
call_split See protocol

[…] imulation procedures. As the starting point, crystal structure and docked structure of GRP78 protein alone, GRP78 with ATP and EGCG inhibitor were used as inputs. The ligand .pdb file was uploaded to PRODRG 2.5 server and the program was run with zero chirality, full charges and with energy minimization parameters selected. Finally, the ligand topology file was generated. To neutralize the total c […]

call_split

Molecular dynamics simulation (MDS) analysis of Vibrio cholerae ToxT virulence factor complexed with docked potential inhibitors

2018
Bioinformation
PMCID: 5953856
DOI: 10.6026/97320630014101
call_split See protocol

[…] 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 throu […]

library_books

Theoretical and NMR Conformational Studies of β Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units

2018
PMCID: 5883087
PMID: 29644215
DOI: 10.3389/fchem.2018.00091

[…] in 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) followed […]

library_books

Interaction of microtubule depolymerizing agent indanocine with different human αβ tubulin isotypes

2018
PLoS One
PMCID: 5870988
PMID: 29584771
DOI: 10.1371/journal.pone.0194934

[…] t 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 []. The Gaste […]

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

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