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.

Imaris 9.3.1 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 9.3.1

:: DESCRIPTION

Imaris is a scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

::DEVELOPER

Imaris team

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

HotSpot3D 1.8.0 – 3D Hotspot Mutation Proximity Analysis tool

HotSpot3D 1.8.0

:: DESCRIPTION

HotSpot3D can be used to identify the mutation hotspots in the linear 1D sequence and correlates these hotspots with known or potential interacting domains based on both known intermolecular interactions and calculated proximity for potential intramolecular interactions.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HotSpot3D

:: MORE INFORMATION

Citation

Nat Genet. 2016 Aug;48(8):827-37. doi: 10.1038/ng.3586. Epub 2016 Jun 13.
Protein-structure-guided discovery of functional mutations across 19 cancer types.
Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L

ProteinScope 1.0.5 – 3D Protein Structure Viewer

ProteinScope 1.0.5

:: DESCRIPTION

ProteinScope is a free program to view and create animations of Protein Data Bank PDB files.

::DEVELOPER

Mark S. Morris

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  MacOsX

:: DOWNLOAD

ProteinScope

:: MORE INFORMATION

MCQ4Structures 1.6.1 – Computing Similarity of 3D RNA / Protein Structures

MCQ4Structures 1.6.1

:: DESCRIPTION

MCQ4Structures is a tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. Although it has been primarily designed to work with RNA structures, MCQ4Structures can be also applied to proteins (however their representation is restricted to the backbone angles).

::DEVELOPER

Tomasz Żok

:: SCREENSHOTS

MCQ4Structures

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Java

:: DOWNLOAD

 MCQ4Structures

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2017 Oct 23;18(1):456. doi: 10.1186/s12859-017-1867-6.
LCS-TA to identify similar fragments in RNA 3D structures.
Wiedemann J, Zok T, Milostan M, Szachniuk M

BayesPairing – Identifying the presence of 3D Structural Modules from RNA sequences

BayesPairing

:: DESCRIPTION

BayesPairing is an automated, efficient and customizable tool for (i) building Bayesian networks representing RNA 3D modules and (ii) rapid identification of 3D modules in sequences. BayesPairing uses a flexible definition of RNA 3D modules that allows us to consider complex architectures such as multi-branched loops and features multiple algorithmic improvements. BayesPairing can handle a broader range of motifs (versatility) and offers considerable running time improvements (efficiency), opening the door to a broad range of large-scale applications.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C++ Compiler

:: DOWNLOAD

BayesPairing

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2019 Apr 23;47(7):3321-3332. doi: 10.1093/nar/gkz102.
Automated, customizable and efficient identification of 3D base pair modules with BayesPairing.
Sarrazin-Gendron R, Reinharz V, Oliver CG, Moitessier N, Waldispühl J.