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Protein Preparation Wizard specifications


Unique identifier OMICS_18928
Name Protein Preparation Wizard
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Woody Sherman <>

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Publication for Protein Preparation Wizard

Protein Preparation Wizard citations


A persulfidation based mechanism controls aquaporin 8 conductance

PMCID: 5931763
PMID: 29732408
DOI: 10.1126/sciadv.aar5770

[…] through the prosa web interface (), where the global quality of each chain was assessed through the z score (−5.73, −5.62, −5.69, and −5.58) (fig. s5b). the model was then refined exploiting the protein preparation wizard, available in maestro software package (): hydrogens were added; the orientation of the hydroxyl groups of ser, thr, and tyr and the side chains of asn and gln residues […]


Mutations Conferring Increased Sensitivity to Tripartite Motif 22 Restriction Accumulated Progressively in the Nucleoprotein of Seasonal Influenza A (H1N1) Viruses between 1918 and 2009

PMCID: 5885024
PMID: 29624498
DOI: 10.1128/mSphere.00110-18

[…] a virus np (pdb codes 2iqh [] and 4bbl []). models and missing loops were generated using the swiss-model web server ( (). structures were then refined with the protein preparation wizard available in the maestro software package (). hydrogens were added, the orientations of the hydroxyl groups of serine, threonine, and tyrosine were obtained, and the side […]


Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase

PMCID: 5831633
PMID: 29489903
DOI: 10.1371/journal.pone.0193623

[…] between ligands and neuraminidase n1 we used two models, one based on pdb entry 2hu4 with absence of the 150 cavity and one based on pdb entry 2hu0 with open access to the 150 cavity.[] the protein preparation wizard (ppw)16 was used for curating original pdb entries.[] the first pre-processing step ppw automatically assigned bond orders of the ligand and add hydrogens to the protein. […]


Fisetin Confers Cardioprotection against Myocardial Ischemia Reperfusion Injury by Suppressing Mitochondrial Oxidative Stress and Mitochondrial Dysfunction and Inhibiting Glycogen Synthase Kinase 3β Activity

PMCID: 5845518
PMID: 29636855
DOI: 10.1155/2018/9173436

[…] the atomic coordinates of gsk3β complexed with indirubin-3′-monoxime (1q41) were downloaded from the rcsb protein data bank (pdb) []. the downloaded structure was prepared using the protein preparation wizard [], a tool from the maestro software package (maestro v9.3, schrödinger, llc, new york, ny). hetero groups were assigned appropriate bond orders. the formal charges […]


Protein S Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde 3 Phosphate Dehydrogenase Gap in Staphylococcus aureus Under Hypochlorite Stress

PMCID: 5791933
PMID: 27967218
DOI: 10.1089/ars.2016.6897

[…] holo form containing nad [pdb code: 3lvf chain r, ()] as well as the apo form [pdb code: 3lc7 chain o, ()] of the enzyme. before molecular docking, both protein structures were prepared using the protein preparation wizard () in the schrodinger software (release 2016–1) graphical user interface maestro. hydrogen was added according to the protonation states at ph of 7.0 as predicted […]


Effects of protein protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel

PMCID: 5812580
PMID: 29444113
DOI: 10.1371/journal.pone.0191905

[…] the most recent version of smina []. smina is a version of autodock vina which offers a better control over the docking and scoring parameters []. the protein structures were prepared using the protein preparation wizard in the schrodinger software package []. the protonation states were assigned at the ph of 7. protein structures were then saved as pdb files and converted to pdbqt format […]

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Protein Preparation Wizard institution(s)
Schrodinger, Sanali Infopark, Banjara Hills, Hyderabad, Andhra Pradesh, India; Schrodinger, New York, NY, USA

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