Protein Preparation Wizard protocols

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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


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  • person_outline Woody Sherman <>

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Publication for Protein Preparation Wizard

Protein Preparation Wizard in pipelines

PMCID: 5148588
PMID: 27936128
DOI: 10.1371/journal.pone.0167763

[…] lpet and laet ligands were constructed and energy minimized with ligprep and the aqa tripeptide was removed from the crystal structure of the enzyme. the receptor (srte1) was also processed with the protein preparation wizard to add missing side chain atoms and hydrogens, and to perform a restrained, partial energy minimization of the coordinates []. docking grid was generated using glide [,], […]

PMCID: 5260052
PMID: 28155653
DOI: 10.1186/s12859-016-1379-9

[…] minimized 3-d structures of the compounds were generated. the protein ck-1δ used in this study was obtained from protein data bank (pdb id- 3uys). this protein was prepared for docking using the protein preparation wizard of glide []. ck-1δ protein preparation involved capping of termini, removal of water molecules, treatment of disulfides and addition of explicit hydrogen. this was followed […]

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Protein Preparation Wizard in publications

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 […]

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 […]

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. […]

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 […]

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 […]

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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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