Molecular Modelling

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MSI :-
Molecular modeling, analysis and simulation for life and 
material sciences.

Model building and analysis in X ray crystallography.

O :-
O is a general purpose macromolecular modeling program aimed at
the field of protein crystallography. It enables the scientist to model,
build and display macromolecules.   O is a graphical display program
built on top of a versatile database system. O brings into use several
tools, which facilitate the building of models into electron density,
allowing this to be done faster and more correctly. Notably, the
autobuild options greatly enhance the speed of building and
rebuilding molecular models.

A versatile structure analysis program for mutant prediction,
structure verification, molecular graphics and more
by Gert Vriend, EMBL, Germany 

*3*DINAMO :-
Interactive protein alignment and model building

Fold recognition from secondary structure predictions of proteins.

An automated homology modelling method, satisfying several spatial
developed by Andrej Sali, Rockefeller University, USA
MODELLER is available to academic users by anonymous ftp.

-123D :-
Threading based on substitution matrix, secondary structure prediction,
and contact capacity potentials by Alexandrov, while at the National
Cancer Institute, USA

protein folding program developed by Srinivasan & Rose,
John Hopkins University, USA

-Profiles-3D :-
inverse protein folding based on compatability of a sequence with
known folds  developed by Eisenberg and coworkers, UCLA, USA
and available from MSI

ProFit fits one protein structure to another. One can specify subsets
of atoms to be considered, specify zones to be fitted by number,
sequence, or by sequence alignment. It can be downloaded by ftp.

Fold prediction from a single sequence or an aligned sequence set
developed by Mark Johnson, University of Turku, Finland

*3*SOPM :-
Self Optimized Prediction Method for Prediction of Protein Secondary
Structure at IBCP-CNRS, France

Sequence-structure Alignment Using a Statistical Approach Guided
by Experiment
Protein threading with flexible force fields.
Freely available to academic users at

Threads a sequence through a set of folds to find energetically
favourable structures  by Jones and coworkers, University
College, London

-Threading :-
Fold recognition by threading, using empirical energy functions, with
specificity and accuracy checks  by Bryant & his group, NCBI, USA

A platform for integrating threading results with protein family analyses
The binaries of IRIX, SunOS and Linux are available

  -Software links
For Structure determination and analysis at RCSB