I-TASSER SUITE
   (Copyright 2014 by Zhang Lab, University of Michigan, All rights reserved)
                    (Version 3.0, released on 2014/01/24)


What is new in I-TASSER V3.0 compared to I-TASSER V2.1?
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1. Four new protein function prediction programs were added:

   (1) COACH for ligand-binding site, EC number and GO terms prediction.
   (2) COFACTOR for ligand-binding site, EC number and GO terms prediction.
   (3) TM-SITE for ligand-binding site prediction.
   (4) S-SITE for ligand-binding site prediction.

2. Template libraries and programs were separated into independent locations
   for users' convenient update of the package.

3. A script 'download_lib.pl' was provided for easy download of all library files.

4. The names of threading programs were standardized to:
   PPAS, dPPAS, dPPAS2, Env-PPAS, MUSTER, wPPAS, wdPPAS, wMUSTER.

5. An option of '-walltime' was added in 'runI-TASSER.pl' to allow users to specify
   walltime in the simulation. Three new options for function prediction ('LBS',
   'EC' and 'GO' were added as well.

6. Some bugs in 'runI-TASSER.pl' were fixed as reported by users of I-TASSER V2.1.


What is new in I-TASSER V2.1 compared to I-TASSER V2.0?
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1. An option was added to allow users to specify JAVA path in their machine.

2. A number of bugs were fixed including 
      (a) missed program 'addchainid' was added in;
      (b) threading names are unified in 'get_cscore.pl'.


What is new in I-TASSER V2.0 compared to I-TASSER V1.0?
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1. Protein secondary structure prediction is improved.

   In I-TASSER V1.0 package, PSI-pred was used to predict secondary structure 
   of target proteins. PSI-pred is third-party software and users need to 
   download the program from other website, which often creates 
   incompatiobility and mistakes in I-TASSER suite configurations. We recently 
   developed a novel secondary structure prediction (PSSpred) by combining 
   seven neural network predictors from different profile data and parameters.
   The Q3 accuracy of PSSpred is ~3% higher than that of PSI-pred. Moreover, 
   PSSpred is seamlessly integrated with the I-TASSER Suite configurations.

2. New threading programs are integrated.
   
   LOMETS in I-TASSER V1.0 includes five threading programs for protein fold-
   recognition and template identification. In I-TASSER V2.0, three new 
   threading programs with a novel sequence profile generation stratagy are
   added. This helps I-TASSER to detect more broad range of structure templates 
   for the I-TASSER fragment assembly. Accordingly, the average TM-score of 
   the final models in I-TASSER V2.0 is ~5% higher than that by I-TASSER V1.0 
   based on the same template library.

3. More flexible for user-intervened modeling.
   
   Users sometimes have the background or structural information of their 
   targets from experimental or biological analysis. Such information is 
   very valuable for protein structure prediction. In I-TASSER V2.0, users 
   are allowed to specify template, target-template aligments, residue-
   residue contact/distance information to guide the I-TASSER simulations. 
   
   I-TASSER V2.0 also allows users to exclude specific template structures
   and/or the templates homologous to the target at certain distance cutoff. 
   This is often useful for different purpose, e.g. for algorithm benchmark 
   and comparisons. These features are newly added to I-TASSER V2.0.

4. A "light" option is added to allow faster modeling.

   A new option "-light" was implemented in I-TASSER V2.0, which sets the
   maximum time of folding simulation below 5 hours. It can be used for the
   users who wants quick results for large easy targets. For large hard
   targets, full version simulations are needed for the best results.

5. Provide an option for trajectory file deposit.

   Advanced users may be interesed in I-TASSER trajectory data analysis. 
   A new option "-traj" was added in I-TASSER V2.0 to allow users to 
   deposit structural decoys from I-TASSER simulations.

6. Fixing bugs in installation and simulations.

   A number of bugs in the installation and implementation, as reported by
   users of I-TASSER V1.0, have been fixed in I-TASSER V2.0. Please post 
   your questions and comments at 
   http://zhanglab.dcmb.med.umich.edu/forum