Molecular design software is notable software for
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 ...
, that provides special support for developing
molecular model
A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecu ...
s ''de novo''.
In contrast to the usual molecular modeling programs, such as for
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 the ...
and
quantum chemistry
Quantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions ...
, such software ''directly'' supports the aspects related to constructing molecular models, including:
*
Molecular graphics
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and KekulĆ ...
* interactive molecular drawing and
conformational editing
* building polymeric molecules, crystals, and
solvated systems
*
partial charge A partial charge is a non-integer charge value when measured in elementary charge units. Partial charge is more commonly called net atomic charge. It is represented by the Greek lowercase letter šæ, namely šæā or šæ+.
Partial charges are c ...
s development
*
geometry optimization
* support for the different aspects of
force field development
Comparison of software covering the major aspects of molecular design
Notes and references
See also
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*
Molecule editor
A molecule editor is a computer program for creating and modifying representations of chemical structures.
Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ...
*
Molecular modelling
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 sci ...
*
Molecular modeling on GPUs
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
In 2007, NVIDIA introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards ...
*
Protein design
Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (''de novo'' design) or by making calcula ...
*
Drug design
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that acti ...
*
Force field (chemistry)
In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the function ...
*
Comparison of force field implementations
This is a table of notable computer programs implementing molecular mechanics force fields.
See also
*Force field (chemistry)
* List of software for Monte Carlo molecular modeling
*Molecular mechanics
*Molecular design software
*Molecule edito ...
*
Comparison of nucleic acid simulation software
This is a list of notable computer programs that are used for nucleic acids simulations.
See also
References
Computational chemistry software
Software comparisons
Molecular dynamics software
Molecular modelling software
{{sc ...
*
Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
See also
*CarāParrinello molecular dynamics
*Comparison of force-field implementations
*Comparison of nucleic acid simulation software
* ...
*
List of molecular graphics systems
This is a list of notable software systems that are used for visualizing macromolecules.
Key
The tables below indicate which types of data can be visualized in each system:
See also
* Biological data visualization
* Comparison of nucleic ...
*
List of software for Monte Carlo molecular modeling
*
List of software for nanostructures modeling
*
Quantum chemistry computer programs
Quantum chemistry computer programs are used in computational chemistry to implement the methods of quantum chemistry. Most include the HartreeāFock (HF) and some post-HartreeāFock methods. They may also include density functional theory (DF ...
*
Quantitative structure-activity relationship
Quantitative may refer to:
* Quantitative research, scientific investigation of quantitative properties
* Quantitative analysis (disambiguation)
* Quantitative verse, a metrical system in poetry
* Statistics, also known as quantitative analysis ...
External links
molecular design''IUPAC'' term definition.
Journal of Computer-Aided Molecular DesignMaterials modelling and computer simulation codesClick2Drug.org
Directory of in silico (computer-aided) drug design tools.
Journal of Chemical Information and ModelingJournal of Computational Chemistry
Science software
Computational chemistry software
Molecular dynamics software
Molecular modelling software