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.

Gen3D – 3D Genome and Chromosome Structural Model Construction

Gen3D

:: DESCRIPTION

Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Gen3D

:: MORE INFORMATION

Citation

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
Nowotny J, Ahmed S, Xu L, Oluwadare O, Chen H, Hensley N, Trieu T, Cao R, Cheng J.
BMC Bioinformatics. 2015 Oct 23;16(1):338.

GMOL 2 – 3D Genome Structure Visualization

GMOL 2

:: DESCRIPTION

GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

GMOL

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GMOL

:: MORE INFORMATION

InfMod3DGen – Inferential Modeling of 3D Chromatin Structure

InfMod3DGen

:: DESCRIPTION

InfMod3DGen is a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data.

::DEVELOPER

InfMod3DGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 InfMod3DGen

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Apr 30;43(8):e54. doi: 10.1093/nar/gkv100.
Inferential modeling of 3D chromatin structure.
Wang S, Xu J, Zeng J.

Facio 22.1.1 – 3D-Graphics program for Molecular Modeling and Visualization

Facio 22.1.1

:: 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

 Facio

:: 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).

Imaris 8.3 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 8.3

:: DESCRIPTION

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

::DEVELOPER

BITPLANE AG

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

Scipion 1.0.0 – An Image Processing Framework for 3D Electron Microscopy

Scipion 1.0.0

:: 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.