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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


No version available


  • person_outline Alessandro Pedretti

Publications for VEGA ZZ

VEGA ZZ citations


Combining agent based models and virtual screening techniques to predict the best citrus derived vaccine adjuvants against human papilloma virus

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

[…] ata 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 […]


Molecular docking analysis of nitisinone with homogentisate 1,2 dioxygenase

PMCID: 5498778
PMID: 28690378
DOI: 10.6026/97320630013136
call_split See protocol

[…] th 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 (http://fafdrugs3.mti.univ-paris-di […]


Structure based comprehensive modelling, spatial fingerprints mapping and ADME screening of curcumin analogues as novel ALR2 inhibitors

PLoS One
PMCID: 5388491
PMID: 28399135
DOI: 10.1371/journal.pone.0175318
call_split See protocol

[…] sent 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 to att […]


PreImplantation factor (PIF) protects cultured embryos against oxidative stress: relevance for recurrent pregnancy loss (RPL) therapy

PMCID: 5464799
PMID: 28423690
DOI: 10.18632/oncotarget.16028

[…] 16F16 molecular structure (obtained as SDF file) and oxidized and reduced forms of PDI (obtained as PDBs 4EL1 and 4EKZ) were prepared (VEGA ZZ, UCSD Chimera PDB2PQR) as model files suitable for virtual docking using AutoDock Vina ( Both were subject to unbiased ligand-receptor docking in full molecular space […]


Insight into SNPs and epitopes of E protein of newly emerged genotype I isolates of JEV from Midnapur, West Bengal, India

BMC Immunol
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 a […]


A synaptotagmin suppressor screen indicates SNARE binding controls the timing and Ca2+ cooperativity of vesicle fusion

PMCID: 5617632
PMID: 28895532
DOI: 10.7554/eLife.28409.042
call_split See protocol

[…] loying 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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