PDBjViewer 4.5.5 – Display 3D Molecular Graphics of Proteins and Nucleic Acids

PDBjViewer 4.5.5

:: DESCRIPTION

PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids.

::DEVELOPER

PDBjViewer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java
  • JOGL

:: DOWNLOAD

 PDBjViewer

:: 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.

LigandScout 3.12 – Pharmacophore 3D Modeling

LigandScout 3.12

:: 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

Inte:Ligand

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

LigandScout

:: 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.

MolIDE 1.7 – Protein 3D Homology Modeling

MolIDE 1.7

:: DESCRIPTION

MolIDE is an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in modeling: sequence search, secondary structure prediction, multiple-round psiblast alignments, assisted alignment editing (integrating a template viewer and secondary structure prediction), side chain replacement and loop building. MolIDE takes an input target sequence and uses PSIBLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target–template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • SCWRL

:: DOWNLOAD

MolIDE

:: MORE INFORMATION

Citation

Qiang Wang, Adrian A Canutescu & Roland L Dunbrack Jr
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
Nature Protocols 3:1832-1847 (2008)

Scipion 2.0 – An Image Processing Framework for 3D Electron Microscopy

Scipion 2.0

:: DESCRIPTION

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers.

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Xmipp

:: DOWNLOAD

  Scipion

:: MORE INFORMATION

Citation:

Scipion: a software framework toward integration, reproducibility and validation in 3D Electron Microscopy.
de la Rosa-Trevín JM, Quintana A, Del Cano L, Zaldívar A, Foche I, Gutiérrez J, Gómez-Blanco J, Burguet-Castell J, Cuenca-Alba J, Abrishami V, Vargas J, Otón J, Sharov G, Vilas JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM.
J Struct Biol. 2016 Apr 20. pii: S1047-8477(16)30079-X. doi: 10.1016/j.jsb.2016.04.010

A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.
Sorzano CO, Vargas J, de la Rosa-Trevín JM, Otón J, álvarez-Cabrera AL, Abrishami V, Sesmero E, Marabini R, Carazo JM.
J Struct Biol. 2015 Mar;189(3):213-9. doi: 10.1016/j.jsb.2015.01.009.

EM-SURFER – Navigating 3D Electron Microscopy Maps

EM-SURFER

:: 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

  • Web browser

:: DOWNLOAD

 NO

:: 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.

VRMLGen 1.4.6 – An R Package for 3D Data Visualization on the Web

VRMLGen 1.4.6

:: DESCRIPTION

VRMLGen is a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language

::DEVELOPER

VRMLGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

VRMLGen

:: 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

ShaEP 1.3.0 – Align Two Rigid 3D Molecular Structure Models

ShaEP 1.3.0

:: 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

  • Windows / Linux / MacOsX

:: DOWNLOAD

 ShaEP

:: 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.

Balloon 1.6.9 – Creates 3D Atomic Coordinates from Molecular Connectivity

Balloon 1.6.9

:: DESCRIPTION

Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.

::DEVELOPER

Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 Balloon

:: MORE INFORMATION

Citation:

J. Santeri Puranen, Mikko J. Vainio, and Mark S. Johnson (2010)
Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery.
Journal of Computational Chemistry, 31, 1722 – 1732.

Phylo-HMRF – Comparing 3D Genome Organization in Multiple Species

Phylo-HMRF

:: DESCRIPTION

Phylo-HMRF (Phylogenetic Hidden Markov Random Field model) identifies evolutionary patterns of 3D genome based on multi-species Hi-C data.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

Phylo-HMRF

:: MORE INFORMATION

Citation

Cell Syst. 2019 Jun 26;8(6):494-505.e14. doi: 10.1016/j.cels.
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.
Yang Y, Zhang Y, Ren B, Dixon JR, Ma J.