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Dock 6.8 has been released

 

This is a new release of DOCK with updated scoring functions including the new pharmacophore matching similarity score and a completely revamped Descriptor Score that allows for different combinations of various scoring functions to be used simultaneously From the readme

NEW IN DOCK 6.8

New Scoring Functions Two new scoring functions were added: pharmacophore score [1], and descriptor score [see the manual].

Pharmacophore: Calculates the pharmacophore overlap between a candidate and a reference molecule. In addition, the python wrapper, mol2bild.py, can be employed to visualize the pharmacophores.

Descriptor Score: Descriptor Score was completely overhauled. Presently, descriptor score is now a wrapper that allows multiple scoring functions to be employed simultaneously. Please refer to the manual for the complete list of scoring functions supported by descriptor score.

Four similarity-based scoring functions were added as part of descriptor score: pharmacophore score, Tanimoto score, Hungarian matching similarity score, and volume overlap score. Hungarian matching similarity score, Tanimoto score and volume overlap score, new to DOCK, can only be called using descriptor score.

Internal Energy Scoring Function Optimization of the internal energy scoring function code and the addition of two parameters:

a) The code has been optimized for calculating the repulsive VDW term. "internalenergyrep_exp", when set to its default value of 12, results in a significant speedup in certain cases. Values other than 12 are computed as in previous versions of DOCK.

b) The term "internalenergycutoff" has been added such that all conformers with an internal energy greater than the cutoff are pruned.

c) The addition of the term "pruningconformerscorescalingfactor", a divisor of the pruningconformerscore_cutoff, ensures that pruning becomes more stringent as flexibly-grown molecules proceed layer-by-layer.

Miscellaneous DOCK now supports builds using Intel compilers with either MPICH2 or Intel MPI parallelism.


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