Sybyl-X protocols

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Sybyl-X specifications


Unique identifier OMICS_19057
Name Sybyl-X
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Maintained Yes


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Sybyl-X in pipeline

PMCID: 5735069
PMID: 29311926
DOI: 10.3389/fphar.2017.00917

[…] hematoxylin and eosin solution and the invading cells were photographed and counted., to investigate the binding of inua-mdm2, inua-mdmx, and inua-nfat1, molecular docking was carried out using the sybyl-x 2.0 software program (tripos associates, inc., st. louis, mo, united states). the structure of inua was constructed using the sybyl/sketch module and optimized via powell’s method […]

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Sybyl-X in publications

PMCID: 5862716
PMID: 29564572
DOI: 10.1186/s13065-018-0401-x

[…] protocol and y-randomization were performed on the training set for internal validation of the obtained models.fig. 1 table 1*test set, *test set, all modeling studies were performed using the sybyl-x 2.0 molecular modeling package (tripos inc., st. louis, usa) running on a windows 7, 32 bit workstation. three-dimensional structures were built using the sketch option in sybyl. […]

PMCID: 5861068
PMID: 29559660
DOI: 10.1038/s41598-018-22894-6

[…] to alter a wide range of properties, including physical attributes, efficacy, bioavailability, and spectrum., the x-ray structure of spinosyn a (1) was minimized using the mmff94 force field– in sybyl-x 2.1.1 (minimization-method = powell, min-energy-change = 0.00001, dielectric = 2.0*r, maximum-iterations = 1000000). default values were used for all other variable parameters. the ethyl […]

PMCID: 5877757
PMID: 29562629
DOI: 10.3390/ijms19030896

[…] converted to pic50; these pic50 values served as the dependent variable, while the descriptor values of comsia and topomer comfa served as the dependent variables. the sketch function in software sybyl x2.0 (certara, princeton, nj, usa) was utilized to draw the structure of the compound, and these 77 molecules were divided in a ratio of 75:25 by sybyl x2.0 in such a way that both datasets […]

PMCID: 5856838
PMID: 29549274
DOI: 10.1038/s41598-018-22914-5

[…] before. the modeled structure was submitted to the structure analysis and verification server (saves) ( as well as protein structure preparation tool of sybyl-x (version 2.1). no bad contacts were noted in the structures. the backbone torsion angles were checked by ramachandran plot for allowed conformations of ϕ and φ angles. all angles […]

PMCID: 5885017
PMID: 29547094
DOI: 10.1099/mgen.0.000165

[…] and related penicillin-binding proteins (pdb ids: 3equ, 3oc2, 3pbq, 3pbn, 3ue3, 4bpj and 5ens; sequence identity 43–87 %), respectively. the models were then minimized using the mmf94s forcefield in sybyl-x 2.1.1 (certara), with the final structures having more than 95 % of residues in the allowed region of a ramachandran plot. meropenem was docked into the models using glide (schrodinger), […]

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