Developing Science Gateways at Various Levels of Granularity Using WS-PGRADE/gUSE - Science Gateways for Distributed Computing Infrastructures - page 108

WS-PGRADE/gUSE supports the development of science gateways at four
different levels of granularity. These levels are:

1. Out of the box: Deploy the generic WS-PGRADE/gUSE framework and pro-
vide it for end-users.

2. Predeveloped workflows: Deploy the generic WS-PGRADE/gUSE framework
and also predevelop and provide the necessary workflows to be executed by the
end-users.
3. End-user view: Use the end-user view of WS-PGRADE/gUSE to hide the
complexity of workflow creation and parameterisation from the end-user.
4. Custom user interface: Develop a completely customized gateway using the
Application-Speci

“ out of the box ”

c Module (ASM) API or the Remote API (Balasko 2013) of
the WS-PGRADE/gUSE framework.

The effort required from application developers and system administrators to
create and set up a gateway increases as we move from option 1 toward option 4,
with the lowest level of developer/system administrator effort being required for the

first option. On the other hand, the level of effort and expertise required from the
end-user decreases signi

cantly as we move toward option 4. The remaining part of
this chapter analyses and describes the different options via the example of a
molecular docking gateway.

8.3 A Gateway for Molecular Docking

Molecular docking simulation programs have signi cant potential to contribute to a

wide area of molecular and biomedical research, including drug design, environ-
mental studies, or psychology. AutoDock (Morris 1998) is one example of a pro-
gram which allows in silico modeling of intermolecular interactions. Emerging
literature shows that AutoDock can be successfully utilized in research strategies
for the study of molecular interactions in cancer (Ali 2007) and for designing drug
inhibitors for HIV (Teixeira 2007), for example. AutoDock is a suite of automated
docking tools. It is designed to predict how small molecules, such as substrates or
drug candidates, bind to a receptor of known 3D structure. AutoDock currently
comprises two discrete generations of software: AutoDock 4 and AutoDock Vina.
The latter provides several enhancements over the former, increasing average
simulation accuracy while also being up to two orders of magnitude faster.
Autodock Vina is particularly useful for virtual screening, whereby a large set of
ligands can be compared for docking suitability with a single receptor. In this
instance parallelism is achieved by first breaking the set of all ligands into equal

sized disjoint subsets. Each computing job then uses a different subset as an input.
The ligands in each subset are simulated/docked sequentially on the computing
node using the single receptor, while a postprocessing stage can be used to compare
the results from all computing jobs.