PONDEROSA-CS 2018 – Determine Protein 3D Structures

PONDEROSA-CS 2018

:: DESCRIPTION

PONDEROSA-CS (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments with Client/Server ) is a new software package for automated protein 3D structure determination.

::DEVELOPER

NMRFAM (National Magnetic Resonance Facility At Madison)

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Server

:: DOWNLOAD

PONDEROSA-CS

:: MORE INFORMATION

Citation

J Biomol NMR. 2014 Nov;60(2-3):73-5. doi: 10.1007/s10858-014-9855-x. Epub 2014 Sep 5.
PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.
Lee W1, Stark JL, Markley JL.

Bioinformatics. 2011 Jun 15;27(12):1727-8. doi: 10.1093/bioinformatics/btr200. Epub 2011 Apr 21.
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.
Lee W1, Kim JH, Westler WM, Markley JL.

3DChrom – Reconstruct Chromosome 3D Structures using Multidimensional Scaling

3DChrom

:: DESCRIPTION

Given a symmetric Hi-C contact matrix, 3DChrom can reconstruct three-dimensional (3D) structures of chromatins or topologically associating domains (TADs)

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Liu T, Wang Z.
Exploring the 2D and 3D structural properties of topologically associating domains.
BMC Bioinformatics. 2019 Dec 2;20(Suppl 16):592. doi: 10.1186/s12859-019-3083-z. PMID: 31787081; PMCID: PMC6886161.

Molecule World DNA Binding Lab 1.1.1 / Molecule World 2.2.0 – Viewing Molecular and Chemical 3d Structures

Molecule World DNA Binding Lab 1.1.1 / Molecule World 2.2.0

:: DESCRIPTION

The Molecule World DNA binding lab is a molecular modeling laboratory that helps students learn about the structure of DNA and explore the diverse types of molecules that bind to DNA.

Molecule World puts 3D chemicals, proteins, DNA, and RNA at your fingertips. Turn molecules around. Make them larger or smaller.

::DEVELOPER

Digital World Biology LLC

:: SCREENSHOTS

:: REQUIREMENTS

iPad

:: DOWNLOAD

Molecule World DNA Binding Lab / Molecule World

:: MORE INFORMATION

SRS3D 1.4 – System for Displaying 3D Structures integrated with Sequences and Features

SRS3D 1.4

:: DESCRIPTION

SRS 3D is a system for displaying 3D structures integrated with sequences and features.

::DEVELOPER

Seán O’Donoghue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux /MacOsX
Java
Java 3D

:: DOWNLOAD

SRS3D

:: MORE INFORMATION

Citation

Seán I. O’Donoghue, Joachim E. W. Meyer, Andrea Schafferhans and Karsten Fries
The SRS 3D module: integrating structures, sequences and features
Bioinformatics (2004) 20 (15): 2476-2478.