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Gen3D specifications


Unique identifier OMICS_11391
Name Gen3D
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Jianlin Cheng

Publication for Gen3D

Gen3D citations


A Novel Workflow to Enrich and Isolate Patient Matched EpCAMhigh and EpCAMlow/negative CTCs Enables the Comparative Characterization of the PIK3CA Status in Metastatic Breast Cancer

Int J Mol Sci
PMCID: 5618534
PMID: 28858218
DOI: 10.3390/ijms18091885

[…] EpCAMlow/negative CTCs which were not captured by the EpCAM-specific ferrofluid used during the CellSearch®-approach.Blood samples were pumped through a disposable cassette (Cell Separation Cassette GEN3D6.5, ANGLE plc) containing narrow passages of 6.5µm in height blocking flow-through of cells larger than most white blood cells—among them CTCs. By virtue of a priming protocol—which flushes each […]


A novel microfluidic platform for size and deformability based separation and the subsequent molecular characterization of viable circulating tumor cells

Int J Cancer
PMCID: 5069649
PMID: 26789903
DOI: 10.1002/ijc.30007

[…] ibed in this article employed a single use, disposable cassette that incorporates the separation method in a design suited to capture of CTCs from blood (ANGLE North America, Cell Separation Cassette GEN3D10, Figs. a–c). The cassette is used in conjunction with a specially developed fluidic processor (ANGLE North America, Parsorter PR1, Fig. d) that generates controlled fluid flow during blood sep […]


Draft Genome Sequence of a Papaverine Degrading, Gram positive Arthrobacter sp., Isolated from Soil Near Hohenheim, Germany

Genome Announc
PMCID: 4440947
PMID: 25999567
DOI: 10.1128/genomeA.00422-15

[…] zTaxon-e databank ().The Glimmer program () was used to search for open reading frames (ORFs) coding for oxygenases within the scaffold sequences. The ORFs were blasted against the NCBI nonredundant, Gen3D, SMART, Pfam, TIGRFam, SUPERFAMILY, HAMP, PIRSF, COILS, and InterProScan databases. Out of a total of 4,599 proteins, the global annotation revealed 11 monooxygenases and 4 α-subunits of Rieske […]


Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated from Uncontaminated Soil in Ecuador

Genome Announc
PMCID: 4432328
PMID: 25977422
DOI: 10.1128/genomeA.00420-15

[…] (13 kb). Remaining scaffolds range below 10 kb or contain gaps.To search for open reading frames (ORFs), the Glimmer program () was used. The ORFs were blasted against the NCBI-nonredundant database, Gen3D, SMART, Pfam, TIGRFam, SUPERFAMILY, HAMP, PIRSF, COILS, and InterProScan. Out of 3,520 identified proteins, 18 ORFs coding for α-subunits of RHOs were found, showing only low identity (<36%) to […]


Cinfony – combining Open Source cheminformatics toolkits behind a common interface

Chem Cent J
PMCID: 2646723
PMID: 19055766
DOI: 10.1186/1752-153X-2-24

[…] abel, these new methods simplify the process of generating 3D coordinates. Compare a single call to make3D() in Cinfony with the following OpenBabel code:structuregenerator = openbabel.OBOp.FindType('Gen3D')structuregenerator.Do(mol)mol.AddHydrogens()ff = openbabel.OBForceField.FindType("MMFF94")ff.Setup(mol)ff.SteepestDescent(50)ff.GetCoordinates(mol)The Cinfony API is identical for all of the to […]


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Gen3D institution(s)
Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO, USA
Gen3D funding source(s)
This work was supported by the National Science Foundation [grant DBI1149224].

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