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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

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

[…] ated 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 were […]


Improvement of kynurenine aminotransferase II inhibitors guided by mimicking sulfate esters

PLoS One
PMCID: 5915280
PMID: 29689093
DOI: 10.1371/journal.pone.0196404
call_split See protocol

[…] rmed using the Impref utility in IMPACT (Schrodinger LLC) and the OPLS-2005 [] force field, and hydrogen atoms were also added and water molecules not involved in the reaction were removed, using the protein preparation wizard in Maestro version 10.4.017 (Schrodinger LLC). The active site was determined by the location of kynurenine in the crystal structure. The ligands were prepared using LigPrep […]


Structural Insight Into the Role of Mutual Polymorphism and Conservatism in the Contact Zone of the NFR5–K1 Heterodimer With the Nod Factor

Front Plant Sci
PMCID: 5909492
PMID: 29706972
DOI: 10.3389/fpls.2018.00344

[…] ber of unique translated sequences was 30. A total of 30 models of the K1 receptor were built by SWISS-MODEL server based on the AtCERK1 template (PDB code: 4EBZ).Each model structure was prepared by Protein Preparation Wizard in Schrödinger 2016-3 software following its Protein Preparation guideline (Sastry et al., ). The structures were refined by minimization subjected to the OPLS2005 force fie […]


Mechanistic Insights into the Stimulant Properties of Novel Psychoactive Substances (NPS) and Their Discrimination by the Dopamine Transporter—In Silico and In Vitro Exploration of Dissociative Diarylethylamines

Brain Sci
PMCID: 5924399
PMID: 29642450
DOI: 10.3390/brainsci8040063

[…] rep module of Schrödinger Release 2017-1 [] with the OPLS3 force field. The prepared compounds all carried a net positive charge as assigned by Epik []. The rDAT homology model was prepared using the Protein Preparation Wizard module in Maestro, following which the Induced fit docking (IFD) protocol, in the Schrödinger software suite was implemented to dock 2-MXP () to the homology model of rDAT. […]


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

[…] fluenza 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 ch […]


Identification of new inhibitors against human Great wall kinase using in silico approaches

Sci Rep
PMCID: 5861128
PMID: 29559668
DOI: 10.1038/s41598-018-23246-0

[…] ttp:// Staurosporine was removed from the active site for docking various compounds of interest. The optimization and minimization of protein was then carried out using Protein Preparation Wizard tool in Schrodinger and OPLS-2005 force field. The tool fixes the protein and makes it suitable for molecular docking. It corrects the incorrect bond orders, charge states, […]


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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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