surface of biomolecules of interest in parallel mode using semi-empirical method.
Molecular Orbital PACkage (MOPAC) is a general purpose semi-empirical
molecular orbital package for the study of molecular structures and their energies
[49]. The high-throughput energy calculations of the small molecules database can
be done by MOPAC using hadoop and cloud technologies. Multiple instances of
MOPAC are created for energy calculations of small molecules database. The tool
can screen a database of millions of small drug-like molecules and understand their
energetics and electrostatic behavior. The tool is useful for finding the target drug
ligands. The torsion angle-driven conformational search method is useful in a range
of chemical design applications [50], including drug discovery and design of targeted chemical hosts. MOSAIC has an easy-to-use interface for the bioinformatics
community over Software as a Service (SaaS) platform. A user-friendly Web
interface has been developed for MOPAC-based energy calculation of small
molecule database. The Web interface has the capability of configuring any
OpenStack-based cloud and managing multiple users to submit the jobs on
dynamically created cloud VM. The Web interface has been developed using
LAMP (Linux, Apache, Mysql, and PHP) framework [51]. The Web interface is
shown in Fig. 9a, b. The application is deployed on OpenStack kilo version which
provides platform for running the MOPAC with resources allocated virtually in the
cloud. OpenStack cloud infrastructure provides scalable computational resources
and scalable storage capacity.
The details of cloud configurations are as follows:
The cloud infrastructure is installed using multi-nodes architecture. The cloud
test bed is deployed using following configurations:
• Controller node: 1 processor, 2 GB memory, and 5 GB storage and 2 NIC.
• Network node: 1 processor, 512 MB memory, and 5 GB storage and 3 NIC.
• Compute node: 1 processor, 2 GB memory, and 10 GB storage and 2 NIC.
To synchronize the clusters, there is a need to set up NTP server. The controller
node acts as NTP server, and rest of the network along with compute nodes would
be synchronize with this controller node. All the nodes in the cluster except controller node have mysql client service, and on controller mysql databases have been
installed. Controller node also contains the messaging server for passing message
across the nodes, and we have used the RabbitMQ [52] server. The configuration is
depicted in Fig. 10.
MOSAIC is executed using underlying Open Stack-based cloud to distribute
millions of molecules in .mop format across the cloud nodes. The cloud nodes can
be dynamically scaled to accommodate the computing load. The drug database is in
the sdf format having different conformations of the same molecule and containing
millions of such molecules. The sdf is converted into the desirable input file, i.e., .
mop format which is used by the code for semi-empirical optimizations. The output
files generated are parsed based on the energy value, and a few best optimized
ligand molecules are selected based on the energy profile. The best few optimized
ligands may further be scrutinized for possible drug target. This tool may have
360
R. R. Joshi et al.
Molecular Orbital PACkage (MOPAC) is a general purpose semi-empirical
molecular orbital package for the study of molecular structures and their energies
[49]. The high-throughput energy calculations of the small molecules database can
be done by MOPAC using hadoop and cloud technologies. Multiple instances of
MOPAC are created for energy calculations of small molecules database. The tool
can screen a database of millions of small drug-like molecules and understand their
energetics and electrostatic behavior. The tool is useful for finding the target drug
ligands. The torsion angle-driven conformational search method is useful in a range
of chemical design applications [50], including drug discovery and design of targeted chemical hosts. MOSAIC has an easy-to-use interface for the bioinformatics
community over Software as a Service (SaaS) platform. A user-friendly Web
interface has been developed for MOPAC-based energy calculation of small
molecule database. The Web interface has the capability of configuring any
OpenStack-based cloud and managing multiple users to submit the jobs on
dynamically created cloud VM. The Web interface has been developed using
LAMP (Linux, Apache, Mysql, and PHP) framework [51]. The Web interface is
shown in Fig. 9a, b. The application is deployed on OpenStack kilo version which
provides platform for running the MOPAC with resources allocated virtually in the
cloud. OpenStack cloud infrastructure provides scalable computational resources
and scalable storage capacity.
The details of cloud configurations are as follows:
The cloud infrastructure is installed using multi-nodes architecture. The cloud
test bed is deployed using following configurations:
• Controller node: 1 processor, 2 GB memory, and 5 GB storage and 2 NIC.
• Network node: 1 processor, 512 MB memory, and 5 GB storage and 3 NIC.
• Compute node: 1 processor, 2 GB memory, and 10 GB storage and 2 NIC.
To synchronize the clusters, there is a need to set up NTP server. The controller
node acts as NTP server, and rest of the network along with compute nodes would
be synchronize with this controller node. All the nodes in the cluster except controller node have mysql client service, and on controller mysql databases have been
installed. Controller node also contains the messaging server for passing message
across the nodes, and we have used the RabbitMQ [52] server. The configuration is
depicted in Fig. 10.
MOSAIC is executed using underlying Open Stack-based cloud to distribute
millions of molecules in .mop format across the cloud nodes. The cloud nodes can
be dynamically scaled to accommodate the computing load. The drug database is in
the sdf format having different conformations of the same molecule and containing
millions of such molecules. The sdf is converted into the desirable input file, i.e., .
mop format which is used by the code for semi-empirical optimizations. The output
files generated are parsed based on the energy value, and a few best optimized
ligand molecules are selected based on the energy profile. The best few optimized
ligands may further be scrutinized for possible drug target. This tool may have
360
R. R. Joshi et al.