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PDB2PQR specifications

Information


Unique identifier OMICS_14370
Name PDB2PQR
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A PDB file.
Input format PDB
Output data A parameterized PQR file and, optionally, an APBS input file.
Output format PQR
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 2.1.1
Stability Stable
Maintained Yes

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Publications for PDB2PQR

PDB2PQR citations

 (321)
call_split

Structural basis for the activation of acid ceramidase

2018
Nat Commun
PMCID: 5915598
PMID: 29692406
DOI: 10.1038/s41467-018-03844-2
call_split See protocol

[…] r Graphics System, Version 1.3 Schrödinger, LLC). No density for ceranib-2 was observed in the electron density of human-aCDase. Calculation of protein side chain pKa values was carried out using the PDB2PQR server. […]

call_split

PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly β(1,6) N acetylglucosamine and can disrupt bacterial biofilms

2018
PLoS Pathog
PMCID: 5933820
PMID: 29684093
DOI: 10.1371/journal.ppat.1006998
call_split See protocol

[…] y using the TLSMD web server [, ]. Structure figures were generated using PYMOL Molecular Graphics System (DeLano Scientific, http://www.pymol.org/), quantitative electrostatics were calculated using PDB2PQR [, ] and APBS [], and conservation levels were generated with ConSurf []. Programs used for crystallographic data processing and analysis were accessed through SBGrid []. […]

library_books

In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design

2018
Nat Commun
PMCID: 5902452
PMID: 29662055
DOI: 10.1038/s41467-018-03746-3

[…] rsion of pdb files into pqr files was perfomed by the utility PDB2PQR using the AMBER force field. The grid dimensions for Adaptive Poisson-Boltzmann Solver (APBS) calculation were also determined by PDB2PQR. Solvation potential energy was calculated by APBS. Surface visualization was performed using the APBS plugin for PyMOL. […]

library_books

Targeting the polyadenylation factor EhCFIm25 with RNA aptamers controls survival in Entamoeba histolytica

2018
Sci Rep
PMCID: 5890266
PMID: 29632392
DOI: 10.1038/s41598-018-23997-w

[…] ls included in GROMACS software. RMSD (root mean square deviation) and RMSF (root mean square fluctuations) values of Cα backbone were calculated. The electrostatic potential was determined using the PDB2PQR server and the APBS software package (http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/). The simulation trajectory was visualized in the VMD 1.9.3 beta1 software (http://www.ks.uiuc.edu/Research/vmd/). […]

call_split

Extracellular loops 2 and 3 of the calcitonin receptor selectively modify agonist binding and efficacy

2018
PMCID: 5908784
PMID: 29454620
DOI: 10.1016/j.bcp.2018.02.005
call_split See protocol

[…] CTR:sCT and CTR:hCT complexes were prepared for molecular dynamics simulations by means of a multistep procedure that integrates both python htmd and tcl (Tool Command Language) scripts. The pdb2pqr and propka software were used to check the protein’s structural integrity and to add hydrogen atoms (configurations of titratable amino acid side chains were visually inspected) appropriate […]

library_books

A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor binding site

2018
Nat Commun
PMCID: 5871881
PMID: 29593268
DOI: 10.1038/s41467-018-03663-5

[…] ar replacement model, the structure was rebuilt using Coot, and refined using Refmac5 (ref. ). Ramachandran statistics were calculated using MolProbity. Electrostatics calculation was performed using PDB2PQR Server using Amber forcefield. […]

Citations

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PDB2PQR institution(s)
Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, St. Louis, MO, USA; Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany; Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA; School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland; Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
PDB2PQR funding source(s)
This work was supported by NIH grant GM069702 and the National Biomedical Computation resource (NIH P41 RR08605); NSF grant MCB 0209941; a Science Foundation Ireland PIYRA grant (04/YI1/M537); the bilateral CERC3 program of CNRS and DFG (KL 1204/3).

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