YASARA 19.9.16 – Molecular Graphics, Modeling & Simulation program

YASARA 19.9.16

:: DESCRIPTION

YASARA (Yet Another Scientific Artificial Reality Application)is a molecular-graphics, -modeling and -simulation program.With an intuitive user interface, photorealistic graphics and support for affordable shutter glasses, autostereoscopic displays and input devices, YASARA creates a new level of interaction with the ‘artificial reality’, that allows you to focus on your goal and forget about the details of the program.

YASARA View is available for free and contains the basic functions you need to explore a macromolecular structure interactively, comparable to other molecule viewers.

YASARA Model contains YASARA View and adds all the functions you need to explore, analyze and model small and macromolecules in a production environment. This includes many features you often miss: unlimited undo/redo, macro recorder, quad-buffered stereo with shutter glasses or the DTI virtual window .

YASARA Dynamics contains YASARA Model and adds support for molecular simulations.

YASARA Structure contains YASARA Dynamics and adds all the functions needed to predict and validate macromolecular structures, including ligand docking and highly accurate force fields with knowledge-based potentials, and an optional module for NMR structure determination.

::DEVELOPER

YASARA Biosciences

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

YASARA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 4. pii: btu426.
YASARA View – molecular graphics for all devices – from smartphones to workstations.
Krieger E1, Vriend G

Bioinformatics. 2002 Feb;18(2):315-8.
Models@Home: distributed computing in bioinformatics using a screensaver based approach.
Krieger E, Vriend G.

PDBjViewer 4.4.4 – Display 3D Molecular Graphics of Proteins and Nucleic Acids

PDBjViewer 4.4.4

:: DESCRIPTION

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

::DEVELOPER

Kengo Kinoshita (Graduate School of Information SciencesTohoku University) and Haruki Nakamura (IPROsaka University)

:: 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.

XtalView 4.0 – Molecular Graphics Program

XtalView 4.0

:: DESCRIPTION

XtalView is a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model. It runs on Sun, DEC, SGI, IBM and PC/Linux computers and takes full advantage of the modern workstation environment. It has a simple but comprehensive windows based interface. The xtalmgr, the main menu drives a suite of crystallographic modules by click of an icon. XtalView maintains log files of the computations done. Standard file formats are used, which facilitates communication between XtalView and programs such as CCP4, X-PLOR, TNT, and MERLOT.

::DEVELOPER

Duncan McRee

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   XtalView

:: MORE INFORMATION

Citation

McRee, D.E. (1999)
XtalView/Xfit – A Versatile Program for Manipulating Atomic Coordinates and Electron Density.
Journal Structural Biology, vol. 125, pp. 156-165.