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 ...
and
macromolecule 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
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHA ...
,
MODELLER
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy ...
,
DELPHI, ZDOCK,
DMol3 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 field (chemi ...
,
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 t ...
,
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 chemistr ...
** For molecular mechanics based simulations: Include implicit and explicit-based solvent models and membrane models
** Also includes the ability to perform hybrid
QM/MM
The hybrid QM/MM (quantum mechanics/molecular mechanics) approach is a molecular simulation method that combines the strengths of ''ab initio'' QM calculations (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processes ...
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
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, foll ...
** 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 cal ...
,
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 Recursive partitioning is a statistical method for multivariable analysis. Recursive partitioning creates a decision tree that strives to correctly classify members of the population by splitting it into sub-populations based on several dichotomous ...
, Genetic Function approximation and 3D field-based QSAR
*
ADME
* 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
*
Protein homology modeling
*
MDL Chime
MDL ''Chime'' was a free plugin used by web browsers to display the three-dimensional structures of molecules. and was based on the RasMol code.
Chime was used by a wide range of biochemistry web sites for the visualization of macromolecules ...
External links
Accelrys.comDiscovery Studio* Supporting free software tools:
Recent News Articles
BioInform (GenomeWeb)
References
{{Chemistry software
Computational chemistry software
Science software