VEGA ZZ protocols

View VEGA ZZ computational protocol

VEGA ZZ statistics

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VEGA ZZ specifications


Unique identifier OMICS_05058
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 3.1.1
Stability Stable
Maintained Yes


  • MetaQSAR


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  • person_outline Alessandro Pedretti <>

Publications for VEGA ZZ

VEGA ZZ in pipelines

PMCID: 4866741
PMID: 27226709
DOI: 10.2147/DDDT.S101929

[…] structure was further evaluated by the molprobity server. finally, ramachandran outliers and poor rotamers were corrected by the wincoot tool., numerous online servers and tools (chemdraw, mcule, vega zz, osiris property explorer, molinspiration, cresset, pymol, discovery studio, autodocktools, and ucsf chimera 1.6) were utilized to design novel compounds that might potentially inhibit hspb8 […]

PMCID: 4651419
PMID: 26617459
DOI: 10.4137/DTI.S31566

[…] research were molecular operating environment (moe) 2008.10, acd/labs’ chemsketch 12.01, research collaboratory for structural bioinformatics (rcsb) protein data bank (pdb) ligand explorer 4.1.0, vega zz 3.0.5, and toxtree 2.5.0. the materials used in this research are sequence data and 3d structure of envelope protein of denv. these data are available online on national center […]

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VEGA ZZ in publications

PMCID: 5751416
PMID: 29297294
DOI: 10.1186/s12859-017-1961-9

[…] bank (pdb id 3vq2) and enriched with hydrogens, fixing the atom charges using the gasteiger – marsili method [] and the charmm 22 potentials for proteins [], using the characteristics built-in in vega zz package []. the application of namd 2.9 [] allowed to optimize the model in order to decrease the high-energy steric interactions. the final step consisted in the lps removal from the complex […]

PMCID: 5498778
PMID: 28690378
DOI: 10.6026/97320630013136

[…] our macromolecule. in order to modify the top hits, we used hyperchem software. the modifications performed in a way that modified ligands improve in drug likeness properties and binding affinity. vega zz and opernbable gui tools were also used to optimize geometry and format conversion. finally, the rationally designed ligands checked by fafdrugs3 web server […]

PMCID: 5388491
PMID: 28399135
DOI: 10.1371/journal.pone.0175318

[…] molecular modelling studies were accomplished with the use of different software packages namely molegro virtual docker (mvd 6.0.0 2013) [], vlife mds 3.5 [], somfa 2.0.0 [], tsar 3d 3.3 [], and vega zz []. firstly, the structures of data set molecules were drawn using chemdraw ultra 8.0; then these sketched molecules were converted into 3d and subjected to energy minimization […]

PMCID: 5339996
PMID: 28264652
DOI: 10.1186/s12865-017-0197-9

[…] using vmd (visual molecular dynamics) in-built solvate v1.5 plugin [] and subjected for minimization. after 5000 steps of conjugate gradient minimization, trajectory analyses were performed by using vega zz interface [] to select the lowest energy frame of models. the resulted models were then subjected for a series of tests such as stereo-chemical analyses by procheck [] geometric relationship […]

PMCID: 5617632
PMID: 28895532
DOI: 10.7554/eLife.28409.042

[…] the charmm22 force field () with periodic boundary conditions and ewald electrostatics in npt ensemble at 300k with a time-step of 2 fs. the trajectory analysis was performed employing vmd and vega zz (drug design laboratory) software; pymol software was used for visualization, molecular graphics, and illustrations. in production runs, the time-step between trajectory points was 240 ps., […]

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VEGA ZZ institution(s)
Dipartimento di Scienze Farmaceutiche “Pietro Pratesi”, Facolta di Farmacia, Universita degli Studi di Milano, Milano, Italy; University of Lausanne, Switzerland

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