TCNG specifications

Information


Unique identifier OMICS_14125
Name TCNG
Alternative name The Cancer Network Galaxy
Restrictions to use None
Database management system SQLite
Data access File download, Browse
Version 0.14
Maintained Yes

Documentation


Maintainer


  • person_outline Satoru Miyano

Publication for The Cancer Network Galaxy

TCNG citations

 (2)
library_books

Molecular, biochemical and kinetic analysis of a novel, thermostable lipase (LipSm) from Stenotrophomonas maltophilia Psi 1, the first member of a new bacterial lipase family (XVIII)

2018
PMCID: 5806266
PMID: 29456971
DOI: 10.1186/s40709-018-0074-6

[…] epared using the Build and the LigPrep module, respectively. Different conformations were generated with the Advanced Search of ConfGen module, by selecting water as solvent and the truncated Newton (TCNG) method for minimization (100 iterations). A 30 × 30 × 30 Å3 grid box with 10 × 10 × 10 Å3 default inner box was centered onto the catalytic triad (S154, D299, H330). All the output conformers we […]

library_books

Discovery of YopE Inhibitors by Pharmacophore Based Virtual Screening and Docking

2013
ISRN Bioinform
PMCID: 4393062
PMID: 25937949
DOI: 10.1155/2013/640518

[…] m 4 low energy isomers, 1 ring conformation, and 10 conformations per rotatable bond were generated; (d) 50 steps of energy minimization were carried out for the conformers with the truncated Newton (TCNG) method using the OPLS_2005 force field and a distance dependent dielectric constant of 4; (e) conformers with high-energy ionization/tautomer states were automatically removed and the number of […]

TCNG institution(s)
Human Genome Center, Institute of Medical Science, The University of Tokyo, Laboratory of DNA Information Analysis, General Research Building, Minato-ku, Tokyo, Japan; RIKEN Computational Science Research Program, Wako, Saitama, Japan; Department of Molecular Medicine & Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand; Department of Obstetrics & Gynaecology, University of Cambridge, The Rosie Hospital, Cambridge, UK; National Institute for Health Research, Biomedical Research Centre, Cambridge, UK
TCNG funding source(s)
This research was supported in part by Grant-in-Aid for Research and Development Project of the Next Generation Integrated Simulation of Living Matter at RIKEN and MEXT Japan.

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