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Protocols

ParDOCK specifications

Information


Unique identifier OMICS_32470
Name ParDOCK
Alternative name Parallel DOCK
Interface Web user interface
Restrictions to use None
Input data A reference complex (target protein bound to a reference ligand) and a candidate molecule.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline B. Jayaram

Publication for Parallel DOCK

ParDOCK citations

 (11)
call_split

Embelin inhibits TNF α converting enzyme and cancer cell metastasis: molecular dynamics and experimental evidence

2014
BMC Cancer
PMCID: 4210574
PMID: 25336399
DOI: 10.1186/1471-2407-14-775
call_split See protocol

[…] The docking results obtained from Glide were confirmed using AutoDock Suite 4.0 [] and ParDOCK []. For Autodock, the protein molecule was prepared by adding polar hydrogens for correct ionization and tautomeric states of amino acid residues and non-polar hydrogens were then merged-up. G […]

library_books

Conjugation of Benzylvanillin and Benzimidazole Structure Improves DNA Binding with Enhanced Antileukemic Properties

2013
PLoS One
PMCID: 3829952
PMID: 24260527
DOI: 10.1371/journal.pone.0080983

[…] The computer modeling of the four compounds binding to DNA was done using the ParDOCK protocol in web-enabled software at www.scfbio-iitd.res.in/dock []. […]

call_split

A plausible mechanism for the antimalarial activity of artemisinin: A computational approach

2013
Sci Rep
PMCID: 3756341
PMID: 23985481
DOI: 10.1038/srep02513
call_split See protocol

[…] Docking of artemisinin and Fe-artemisinin adduct to PfATP6 was carried out using Pardock. Scoring of these docked structures was done by Bappl. Details of the docking methodology are provided in the . These docked structures were taken as input for molecular dynamics simulations. […]

library_books

Genomes to Hits In Silico A Country Path Today, A Highway Tomorrow: A Case Study of Chikungunya

2013
Curr Pharm Des
PMCID: 3831887
PMID: 23260020
DOI: 10.2174/13816128113199990379

[…] egies (Table ) such as Sanjeevini (http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp) to identify a few candidates which could be pursued as leads for experimental synthesis and validation [,]. ParDOCK module of Sanjeevini is an all-atom energy based Monte Carlo algorithm for protein-ligand docking. It involves the positioning of ligands optimally with best configuration in the protein bindi […]

library_books

Prediction of Functional Loss of Human Angiogenin Mutants Associated with ALS by Molecular Dynamics Simulations

2013
Sci Rep
PMCID: 3566597
PMID: 23393617
DOI: 10.1038/srep01225

[…] 54E, F100I, R121C and R121H (). To correlate this change in conformation of catalytic residue His114 with loss of ribonucleolytic activity in certain mutants, docking simulations were performed using ParDOCK. NCI-65828, which is an inhibitor of ribonucleolytic activity of ANG, was used for docking of mutant ANG proteins. Snapshots of ANG mutants were captured at both native and altered His114 conf […]

library_books

Mechanisms of Loss of Functions of Human Angiogenin Variants Implicated in Amyotrophic Lateral Sclerosis

2012
PLoS One
PMCID: 3288110
PMID: 22384259
DOI: 10.1371/journal.pone.0032479

[…] ive conformation possessing ribonucleolytic activity (see ). Similarly, docking between the inhibitor and K17I, S28N, P112L, V113I variants and L35P, K60E mutants were performed using AutoDock , and ParDOCK – and the binding energies for each case were determined and presented (). It was observed that the binding energy in those cases where the dihedral angle of the His114 changes significantly w […]

Citations

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ParDOCK institution(s)
Department of Chemistry & Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, New Delhi, India

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