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University of Modena, with expertise in molecular dynamics for
virtual screening and drug design on malaria
CNR-ITB Institute for Biomedical Technologies in Milano, with
expertise in high-performance and GRID computing applications
for bioinformatics in life sciences
HealthGrid (http://healthgrid.org), with expertise in grid tech-
nology for life sciences and in infrastructure support
Chonnam National University, with expertise in biochemistry
and in vitro validation of virtual screening
KISTI in Korea, with expertise in grid technology
Besides t h i s core g roup, a nu mber of biolog ica l laborator ies have ex pressed
interest to propose targets or to perform in vitro tests of the best molecules
selected in silico :
Mahidol University in Thailand
University of Los Andes in Venezuela
CSIR and University of Pretoria in South Africa
These very satisfactory results obtained both on the biochemical side and
on the grid side of the project should not hide the fact that very signii cant
progress can be achieved on both sides.
The virtual screening pipeline described in Figure 14.2 can be rei ned at
several levels.
In terms of target preparation, it is well known that the PDB is full
of bugs, especially for the structures that have been downloaded
many years ago.
In terms of ligand selection, our approach has been very naïve as
we have been docking all the compounds available in ZINC and
Chembridge. Software packages exist to perform the i rst selec-
tion of the ligands on physical and chemical criteria to reduce the
number of dockings.
The availability of three-dimensional macromolecular coordinates is a
prerequisite for many types of studies. PDB contains many anomalies
ranging from proteins with small deviations from normal geometry, to
structures that i t their submitted experimental data very poorly.
Led by CMBI, a massive rerei nement project was launched to obtain a
better match between the experimental data and the atomic parameters
(coordinates, B-factors) in the structure models while not compromising
the geometric quality of the structure models [25]. The rerei nement of
such a vast number of structure models requires enormous amounts of
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