Discovery Studio is a suite of
software
Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work.
...
for simulating
small molecule
Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are ...
and
macromolecule
A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. ...
systems. It is developed and distributed b
Dassault Systemes BIOVIA(formerly Accelrys).
The product suite has a stron
academic collaboration programme supporting scientific research and makes use of a number of software algorithms developed originally in the scientific community, including
CHARMM,
MODELLER,
DELPHI
Delphi (; ), in legend previously called Pytho (Πυθώ), in ancient times was a sacred precinct that served as the seat of Pythia, the major oracle who was consulted about important decisions throughout the ancient classical world. The oracl ...
, ZDOCK,
DMol3
DMol3 is a commercial (and academic) software package which uses density functional theory with a numerical radial function basis set to calculate the electronic properties of molecules, clusters, surfaces and crystalline solid materials
from fi ...
and more.
Scope
Discovery Studio provides software applications covering the following areas:
* Simulations
** Including
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Mo ...
,
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of th ...
,
Quantum Mechanics
Quantum mechanics is a fundamental theory in physics that provides a description of the physical properties of nature at the scale of atoms and subatomic particles. It is the foundation of all quantum physics including quantum chemistry, q ...
** For molecular mechanics based simulations: Include implicit and explicit-based solvent models and membrane models
** Also includes the ability to perform hybrid
QM/MM calculations
* Ligand Design
** Including tools for
enumerating molecular libraries and library optimization
*
Pharmacophore modeling
** Including creation, validation and
virtual screening
Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme.
Virt ...
*
Structure-based Design
** Including tools for
fragment-based placement and refinement,
receptor-ligand docking and pose refinement, de novo design
* Macromolecule design and validation
* Macromolecule engineering
** Specialist tools for
protein-protein docking
** Specialist tools for
Antibody design[Almagro J.C., Beavers M.P., Hernandez-Guzman F., Maier J., Shaulsky J.,
Butenhof K., Labute P., Thorsteinson N., Kelly K., Teplyakov A., Luo J., Sweet R., Gilliland G.L., Antibody modeling assessment, ''Proteins: Structure, Function, and Bioinformatics'', 2011, 79(11), pages 3050–3066.] and optimization
** Specialist tools for
membrane-bound proteins, including
GPCR
G protein-coupled receptors (GPCRs), also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily-related p ...
s
*
QSAR
** Covering methods such as
multiple linear regression
In statistics, linear regression is a linear approach for modelling the relationship between a scalar response and one or more explanatory variables (also known as dependent and independent variables). The case of one explanatory variable is c ...
,
partial least squares
Partial least squares regression (PLS regression) is a statistical method that bears some relation to principal components regression; instead of finding hyperplanes of maximum variance between the response and independent variables, it finds a li ...
,
recursive partitioning, Genetic Function approximation and 3D field-based QSAR
*
ADME
ADME is an abbreviation in pharmacokinetics and pharmacology for " absorption, distribution, metabolism, and excretion", and describes the disposition of a pharmaceutical compound within an organism. The four criteria all influence the drug l ...
* Predictive toxicity
See also
*
Molecular Mechanics Programs
*
Quantum Mechanics Software
*
Molecular Modeling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scien ...
*
Molecular Design Software Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models ''de novo''.
In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemi ...
*
Protein homology modeling
*
MDL Chime
External links
Accelrys.comDiscovery Studio* Supporting free software tools:
Recent News Articles
BioInform (GenomeWeb)
References
{{Chemistry software
Computational chemistry software
Science software