Support for Cooperative Experiments in e-Science: From Scientific Work flows to Knowledge Sharing - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 152

enable SWMS to use one another's services. However, being able to use services
across multiple SWMSs is just part of the solution as currently there are no common
standards for sharing knowledge associated with the proper use of services, nor is
there a standard for sharing executable workflows. In this chapter we addressed the
issue of knowledge sharing. It is clear that, given the current state of art, knowledge
sharing is very much integrated into or dependent upon the executable workflow
description. We think that knowledge should only be loosely coupled to the system
which generates it, and we propose PFTs as a means to achieve this goal. Through
this loose coupling PFTs can easily be implemented on top of different SWMSs.
Diverse e-Science applications which require different SWMS for their execution
can, by using this construct, share knowledge about the proper use of their web/grid
services more easily.

7.6.1 Prospective Usage Applications

The VL-e framework has been created based on requirements extracted from six
different scientific domains. In this chapter we have given an example of scientific
application developed using the VL-e framework. However, the generic aspects of
this framework make it applicable to various scientific domains including practical
medicine (Leguy et al. 2011 ; Inda et al. 2008 ; Koulouzis et al. 2010 ) . The computer
aided drug design makes possible the creation of new chemical compounds which
can work as the modificators of the “target” molecules creating the complexes
with them. The presence of the ligand - potential drug - may correct the improper
activity of the protein which is the source of the pathological process in patients
body. This is why the VL-e may be implemented into the practical medicine.
The new challenge for practical medicine is the individual therapy. The tradi-
tional diagnostics and therapy stops when particular pathology has been recognized
and particular procedure is applied for therapy. So far there arę some clinical paths
for the group of patients representing similar symptoms. In post-genomic era, when
the SNP (single nucleotide polymorphism) has been recognized and identified the
individual therapy is expected. The drug, which can work successfully in one case
may be useless in the other due to structural changes in proteins being the results of
SNP. This is why the individually created drugs addressed to particular “target”
protein should be applied in therapeutic procedures. New drug design takes time.
The structure of proteins influenced by SNP should be generated and the possible
ligand binding cavities should be recognized as well as possible protein-protein
complexation areas. This time period should be as short as possible to make the
therapy successful. The availability of tools (and methods) described in his topic are
the milestones in respect to these expectations.
The generation of mutation-modified structure of target molecule and
identification of ligand binding cavities (protein-protein complexation) are neces-
sary for correction malfunctioning proteins in the human body. The feature of
individual therapy is applicable to AIDS therapy. HIV virus is characteristic by its