:: DESCRIPTION
MOGEN is a useful tool for converting chromosomal contact data into 3D genome models to provide a better view into the spatial organization of genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MOGEN: A Tool for Reconstructing 3D Models of Genomes from Chromosomal Conformation Capturing Data.
Trieu T, Cheng J.
Bioinformatics. 2015 Dec 31. pii: btv754
:: DESCRIPTION
LJ3D is a computational method to reconstruct high-resolution 3D chromosome structures based on the zero-inflated single-cell Hi-C data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zha,M.Wang,N.Zhang,C and Wang,Z. (2021)
Inferring single-cell 3D chromosomal structures based on Lennard-Jones potential.
International Journal of Molecular Sciences, under review.
:: DESCRIPTION
SuMo (Surfing the Molecules) is a bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2005 Oct 15;21(20):3929-30.
The SuMo server: 3D search for protein functional sites.
Jambon M, Andrieu O, Combet C, Deléage G, Delfaud F, Geourjon C.
:: DESCRIPTION
SketchBio is a tool that incorporates state-of-the-art bimanual interaction and drop shadowsto enable rapid construction of molecular structures and animations
::DEVELOPER
CISMM (Computer Integrated Systems for Microscopy and Manipulation)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014 Oct 30;15(1):334.
SketchBio: a scientist’s 3D interface for molecular modeling and animation.
Waldon SM, Thompson PM, Hahn PJ, Taylor RM 2nd.
:: DESCRIPTION
Facio is an OpenGL-based 3D-graphics program for molecular modeling and visualization of quantum chemical calculations (GAMESS and Gaussian)
Since Facio internally uses PDB (Protein Data Bank) format, it can also display a 3D-structure of biological macromolecules, such as proteins and nucleic acid with emphasizing their secondary or quaternary structures.
::DEVELOPER
Masahiko Suenaga @ Kyushu University
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. Suenaga,
Facio: New Computational Chemistry Environment for PC GAMESS
Journal of Computer Chemistry, Japan, Vol. 4, No. 1 pp. 25-32 (2005).
:: DESCRIPTION
PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2004 May 22;20(8):1329-30. Epub 2004 Feb 10.
eF-site and PDBjViewer: database and viewer for protein functional sites.
Kinoshita K, Nakamura H.
:: DESCRIPTION
LigandScout is a fully integrated platform for accurate virtual screening based on 3D chemical feature pharmacophore models. It offers seamless workflows, starting both from ligand- and structure based pharmacophore modeling, and includes novel high performance alignment algorithms for excellent prediction quality with unprecedented screening speed. Additionally, we have included user-friendly screening analysis tools, including the automated generation of ROC curves for performance assessments. All functions are accessible through a well elaborated graphic user interface that reflects our years of experience in creation of the most user-friendly pharmacophore modeling tools. The algorithms are scientifically validated and based on our well-established knowledge in pharmacophore research, while the application corresponds to state-of-the-art information technology.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wolber, G.; Langer, T.;
LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters.
J. Chem. Inf. Model; 2005; 45(1); 160-169.
:: DESCRIPTION
EM-SURFER is a web platform for real-time electron microscopy database search. It compares isosurface shape of a query EM map against maps in the latest EMDB.
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Navigating 3D electron microscopy maps with EM-SURFER.
Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D.
BMC Bioinformatics. 2015 May 30;16:181. doi: 10.1186/s12859-015-0580-6.
:: DESCRIPTION
VRMLGen is a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
vrmlgen: An R Package for 3D Data Visualization on the Web
Journal of Statistical Software, 2010 DOI: 10.18637/jss.v036.i08
:: DESCRIPTION
ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods.
::DEVELOPER
Structural Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Mikko J. Vainio, J. Santeri Puranen and Mark S. Johnson (2009)
ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential.
J. Chem. Inf. Model. 49, 492-502.
