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5 Complex Reactive Applications: A Forward Look to Open Science
CADDSuite [116] is a code that offers modular tools for most commonly used
tasks in the field of computer-aided drug design, that all have the same interface
and can easily be used to create even complex workflows. There are algorithms
and tools for data storage and retrieval, data preparation, chemical checks, QSAR,
Docking, Rescoring, analysis of results. CADDSuite has also been integrated into the
workflow system Galaxy, in order to make submitting jobs to different environments
or creating, modifying and starting workflows for the user. In essence, a user can
thus easily create drug design pipelines directly from a web browser, without any
need for software installations on his local computer.
FlexX [117] is a code that predicts within a few seconds the geometry of the
protein–ligand complex for a protein with known three-dimensional structure and a
small ligand molecule. The use of an intuitive GUI permits the set up of docking
runs within a single minute and provides you with fast visual feedback. FlexX can
screen a library of 1 000 000 compounds in a few hours on a 30-node cluster. The
new screen module also allows you to filter out false positives on the fly. If you
are screening compounds from a combinatorial library, you can take advantage of
a novel pharmacophore-based combinatorial docking to further gain speed-up and
enrichment.
DESMOND [118] is a computer program that can compute energies and forces
for the standard fixed-charged force fields used in biomolecular simulations. A variety of integrators and support for various ensembles have been implemented in the
code, including methods for thermostatting (Andersen, Nose-Hoover, and Langevin)
and barostatting (Berendsen, Martyna-Tobias-Klein, and Langevin). Ensembles typically used in membrane simulations (constant surface area and surface tension) and
semi-isotropic and fully anisotropic pressure coupling schemes are also available.
Desmond supports algorithms typically used to perform fast and accurate molecular
dynamics. Long-range electrostatic energy and forces are calculated using particlemesh-based Ewald techniques. Constraints, which are enforced using a variant of the
SHAKE algorithm, allow the time step to be increased. These approaches can be used
in combination with time-scale splitting (RESPA-based) integration schemes. The
Desmond software includes tools for minimization and energy analysis (which can
be run efficiently in a parallel environment), methods for restraining atomic positions
as well as molecular configurations, support for generating a variety of periodic cell
configurations, and facilities for creating accurate checkpoints and restart.
AMBER [119] is a code that can compute potential energies for molecular systems
(with particular focus on biosystems) by formulating the related potential energy
as a combination of terms representing covalent bonds (depending on internuclear
distances), bending distortions (depending on planar angles), dihedral and torsional
motions (depending on spatial angles), dispersion effects (depending on Van der
Waals interactions) and electrostatic forces (depending on charges and distances).
The software comes with libraries and databases of parameter values tailored to suit
different molecular systems.
5 Complex Reactive Applications: A Forward Look to Open Science
CADDSuite [116] is a code that offers modular tools for most commonly used
tasks in the field of computer-aided drug design, that all have the same interface
and can easily be used to create even complex workflows. There are algorithms
and tools for data storage and retrieval, data preparation, chemical checks, QSAR,
Docking, Rescoring, analysis of results. CADDSuite has also been integrated into the
workflow system Galaxy, in order to make submitting jobs to different environments
or creating, modifying and starting workflows for the user. In essence, a user can
thus easily create drug design pipelines directly from a web browser, without any
need for software installations on his local computer.
FlexX [117] is a code that predicts within a few seconds the geometry of the
protein–ligand complex for a protein with known three-dimensional structure and a
small ligand molecule. The use of an intuitive GUI permits the set up of docking
runs within a single minute and provides you with fast visual feedback. FlexX can
screen a library of 1 000 000 compounds in a few hours on a 30-node cluster. The
new screen module also allows you to filter out false positives on the fly. If you
are screening compounds from a combinatorial library, you can take advantage of
a novel pharmacophore-based combinatorial docking to further gain speed-up and
enrichment.
DESMOND [118] is a computer program that can compute energies and forces
for the standard fixed-charged force fields used in biomolecular simulations. A variety of integrators and support for various ensembles have been implemented in the
code, including methods for thermostatting (Andersen, Nose-Hoover, and Langevin)
and barostatting (Berendsen, Martyna-Tobias-Klein, and Langevin). Ensembles typically used in membrane simulations (constant surface area and surface tension) and
semi-isotropic and fully anisotropic pressure coupling schemes are also available.
Desmond supports algorithms typically used to perform fast and accurate molecular
dynamics. Long-range electrostatic energy and forces are calculated using particlemesh-based Ewald techniques. Constraints, which are enforced using a variant of the
SHAKE algorithm, allow the time step to be increased. These approaches can be used
in combination with time-scale splitting (RESPA-based) integration schemes. The
Desmond software includes tools for minimization and energy analysis (which can
be run efficiently in a parallel environment), methods for restraining atomic positions
as well as molecular configurations, support for generating a variety of periodic cell
configurations, and facilities for creating accurate checkpoints and restart.
AMBER [119] is a code that can compute potential energies for molecular systems
(with particular focus on biosystems) by formulating the related potential energy
as a combination of terms representing covalent bonds (depending on internuclear
distances), bending distortions (depending on planar angles), dihedral and torsional
motions (depending on spatial angles), dispersion effects (depending on Van der
Waals interactions) and electrostatic forces (depending on charges and distances).
The software comes with libraries and databases of parameter values tailored to suit
different molecular systems.