TINKER :-Molecular modelling
TINKER a molecular
modeling software is a complete and general
package for molecular mechanics and dynamics,
with some special features for polypeptides.
TINKER has the ability to use any of several
common parameter sets, such as AMBER-95,
CHARMM22, MM2(1991), MM3(2000), OPLS-AA and
OPLS-UA.
Tessellator :- Molecular volume visualisation
Tessellator
is
an application for the tessellation of 3D volume
in and around biological molecules. It creates
Tcl script files which are run within
VMD to visualize
volumes in context with their associated
molecular structures
Tonto :- Quantum Chemistry
Tonto is a free
package for doing quantum chemistry simulations.
The main objective of Tonto is to be
simple--simple to understand, simple to use, and
most importantly, simple to hack
VASP :- Vienna Ab-Initio Simulation Package
VASP
is a Fortran90 plane-wave DFT code which can be run
as a single-cpu or MPI-parallel code. It runs on
many platforms, too many in fact for the VASP group
to test and support VASP on all of them. Peter
Klaver ported VASP to MacOSX using LAM-MPI and the
IBM XLF/XLC compilers for MacOSX (now using gcc
instead of XLC for MacOSX 10.4 'Tiger').
Performance is excellent and he has written a 'How
to install+run VASP for dummies'
instruction
Viewmol :-Molecule viewer
Viewmol is a graphical
front end for computational chemistry programs.
It is able to graphically aid in the generation
of molecular structures for computations and to
visualize their results
VMD :-Molecule viewer
VMD 1.8.5 VMD is a
molecular visualization program for displaying,
animating, and analyzing large biomolecular
systems using 3-D graphics and built-in
scripting. VMD supports computers running
MacOS-X,and now uses native windowing and
hardware acceleration. The vmd-xplor package is a
combination of VMD with the xplor structure
determination package
Widgets :- A collection of widgets
XDrawChem :-Structure drawing
XDrawChem is a
two-dimensional molecule drawing program for
Unix operating systems. It is similar in
functionality to other molecule drawing programs
such as ChemDraw (TM, CambridgeSoft). It can
read and write MDL Molfiles, and read ChemDraw
text and binary files, to allow sharing between
XDrawChem and other chemistry applications, and
it can create images in popular formats like PNG
and EPS.
X-score :-Calc binding affinity
X-score is a scoring function that
computes the binding affinities of ligands to a
target protein (Dr. Xueliang Fang and Dr.
Renxiao Wang J. Med. Chem. 2003, 46 2287) whilst
it was written for SGI it compiles fine with
either Apples GCC or the IBM c++
compiler.
Zodiac :- Human steered molecular docking
Zodiac is the result
of work by Nicola Zonta on developing an
environment for human steered computation
approaches to drug design. The application is
built upon OpenBabel and the aim is to use
simple input devices to allow the user to
interact with a molecule and guide it into an
active site. To date they have implemented
haptic device support so you can feel when the
molecule bumps into the receptor, and wiimote
head tracking for 3D visulisation.
The application is still in early development but already has impressive graphics capabilities. In addition Zodiac now includes a front-end to the PLANTS docking engine.
The application is still in early development but already has impressive graphics capabilities. In addition Zodiac now includes a front-end to the PLANTS docking engine.