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OS: Linux, Windows, Mac

YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X developed since 1993, that finally makes it really easy to answer your questions. 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 provides a number of features with unique properties:

Molecular graphics
Molecular movies and eLearning
Molecular dynamics with 4 clicks
nteractive real-time surfaces
New force fields: YASARA , YAMBER, NOVA
pH dependent typing of organic molecules
Fastest molecular dynamics algorithms, see benchmarks
MD simulation of membrane proteins with 4 clicks
Automatic force field parameter assignment for 98% of the PDB
Yanaconda macros and Python scripts
Homology modeling with 4 clicks and CASP approval
Small-molecule docking with 4 clicks
Loop modeling
Side-chain prediction
pH dependent hydrogen bonding networks
Structure validation including ligands
NMR structure determination with 4 clicks
Multi-dimensional knowledge-based potentials

Link: http://www.yasara.com/