Tag: 3D

IMAAAGINE – Search Hypothetical 3D Protein Arrangement in Protein Data Bank

IMAAAGINE

:: DESCRIPTION

The IMAAAGINE (IMagine An Amino Acid 3D pattern search enGINE) program allows users to search for hypothetical amino acid 3D arrangement query to be searched against the PDB. Users design their own motif with specific residue types and distances between residues, with a flexible distance tolerance.

::DEVELOPER

The Molecular Function Regulation Lab (M. Firdaus Raih research group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2013.
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank.
Nucleic Acids Res. 41 (W1): W432-W440

TeraStitcher v1.10.18 – 3D Stitching tool designed for Teravoxel-sized microscopy images

TeraStitcher v1.10.18

:: DESCRIPTION

TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (< 8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently retrieved and processed.

::DEVELOPER

TeraStitcher team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 TeraStitcher

:: MORE INFORMATION

Citation:

BMC Bioinformatics 2012, 13:316
TeraStitcher – A Tool for Fast Automatic 3D-Stitching of Teravoxel-Sized Microscopy Images
Alessandro Bria and Giulio Iannello

RNA-Redesign – Web server for Fixed-backbone 3D Design of RNA

RNA-Redesign

:: DESCRIPTION

RNA-Redesign utilizes fixed-backbone design to optimize the primary sequence of a RNA to match a desired backbone, in analogy to fundamental tools that have driven major advances in protein engineering.

::DEVELOPER

RNA-Redesign team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

RNA-Redesign: a web server for fixed-backbone 3D design of RNA.
Yesselman JD, Das R.
Nucleic Acids Res. 2015 May 11. pii: gkv465.

RNA2D3D 5.7.0 – Conversion of RNA 2D Structures to 3D and 3D Modeling

RNA2D3D 5.7.0

:: DESCRIPTION

RNA2D3D accepts the primary RNA sequence information and a secondary structure representation for the sequence, which may include pseudoknots (Martinez et al. 2008). It rapidly generates a first-pass, three-dimensional model from the secondary structure. Further refinements of the models are usually necessary, but in many cases the first pass model will give significant insights as to how to proceed. Because of its speed and because of the flexibility of its structure editing tools, RNA2D3D can be used to quickly explore alternative 3D conformations in an interactive fashion (Note that it is not a de novo 3D structure prediction program.).

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/SGI/Irix

:: DOWNLOAD

 RNA2D3D

:: MORE INFORMATION

Citation:

J Biomol Struct Dyn. 2008 Jun;25(6):669-83.
RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.
Martinez HM, Maizel JV Jr, Shapiro BA.

DBPnet v0.1.4 – Inferring cooperation of DNA Binding Proteins in 3D genome

DBPnet v0.1.4

:: DESCRIPTION

DBPnet – Inferring cooperation of DNA binding proteins in 3D genome.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOS

:: DOWNLOAD

  DBPnet

:: MORE INFORMATION

Citation

Zhang K, Li N, Ainsworth RI, Wang W.
Systematic identification of protein combinations mediating chromatin looping.
Nat Commun. 2016 Jul 27;7:12249. doi: 10.1038/ncomms12249. PMID: 27461729; PMCID: PMC4974460.

CompuCell3D 4.2.5 – 3D Multiscale Multi-cell Simulations

CompuCell3D 4.2.5

:: DESCRIPTION

CompuCell3D (CC3D) runs 3D multiscale multi-cell simulations, integrating the GGH model , PDE solvers (reaction-diffusion), and cell type automata (differentiation). CompuCell3D runs in parallel with the CompuCellPlayer visualization engine.

CompuCell3D was originally written to model morphogenesis, the process in embryonic development where cells cluster into patterns which eventually differentiate into organs, muscle or bone. Through integration of multiple mathematical models into a software implementation with easy to use XML based syntax scientists were able to build models within few hours as opposed to weeks when writing source code from scratch. compuCell3D is based on Glazier-graner-Hogeweg model (GGH) also known as the Cellular Potts Model (CPM).The model is capable of capturing key cellular behaviors: cell clustering as well as growth, division, death, intracellular adhesion, and volume and surface area constraints;

::DEVELOPER

CompuCell3D Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

 CompuCell3D

:: MORE INFORMATION

Citation

Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier
A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation
PLoS Comput Biol 7(10): e1002155. doi:10.1371/journal.pcbi.1002155

VESTA 3.5.7 – 3D Visualization System for Electronic & Structural Analysis

VESTA 3.5.7

:: DESCRIPTION

VESTA (Visualization System for Electronic & Structural Analysis) is a 3D visualization program for structural models and 3D grid data such as electron/nuclear densities. Some of the novel features of VESTA are listed below.

::DEVELOPER

Koichi Momma

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 VESTA

:: MORE INFORMATION

Citation

K. Momma and F. Izumi,
“VESTA: a three-dimensional visualization system for electronic and structural analysis,”
J. Appl. Crystallogr., 41:653-658, 2008.

Jmol 14.31.44 – Java Viewer for Chemical Structures in 3D

Jmol 14.31.44

:: DESCRIPTION

Jmol is a free, open source molecule web browser applet for chemical structures in 3D for students, educators, and researchers in chemistry and biochemistry.

::DEVELOPER

Jmol Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

Jmol

:: MORE INFORMATION

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