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Molecular design software, the Glossary

Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo.^[1]

44 relations: Abalone (molecular mechanics), AMBER, Ascalaph Designer, BOSS (molecular mechanics), Comparison of force-field implementations, Comparison of nucleic acid simulation software, Comparison of software for molecular mechanics modeling, Discovery Studio, DOCK, Drug design, Firefly (computer program), FoldX, Force field (chemistry), Freeware, Lead Finder, List of molecular graphics systems, List of quantum chemistry and solid-state physics software, List of software for Monte Carlo molecular modeling, List of software for nanostructures modeling, Materials Studio, Mathematical optimization, Molecular dynamics, Molecular graphics, Molecular mechanics, Molecular model, Molecular modeling on GPUs, Molecular modelling, Molecular Operating Environment, Molecule editor, OPLS, Partial charge, Protein design, Quantitative structure–activity relationship, Quantum chemistry, Quantum mechanics, Rosetta@home, SAMSON, Schrödinger, Inc., Scigress, Solvation, Spartan (chemistry software), Tinker (software), Winmostar, XMD.
Molecular dynamics software

Abalone (molecular mechanics)

Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models. Molecular design software and Abalone (molecular mechanics) are computational chemistry software, molecular dynamics software, molecular modelling software and science software.

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AMBER

Assisted Model Building with Energy Refinement (AMBER) is the name of a widely-used molecular dynamics software package originally developed by Peter Kollman's group at the University of California, San Francisco. Molecular design software and AMBER are molecular dynamics software.

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Ascalaph Designer

Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. Molecular design software and Ascalaph Designer are computational chemistry software, molecular dynamics software and molecular modelling software.

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BOSS (molecular mechanics)

Biochemical and Organic Simulation System (BOSS) is a general-purpose molecular modeling program that performs molecular mechanics calculations, Metropolis Monte Carlo statistical mechanics simulations, and semiempirical Austin Model 1 (AM1), PM3, and PDDG/PM3 quantum mechanics calculations. Molecular design software and BOSS (molecular mechanics) are molecular modelling software.

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Comparison of force-field implementations

This is a table of notable computer programs implementing molecular mechanics force fields.

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Comparison of nucleic acid simulation software

This is a list of notable computer programs that are used for nucleic acids simulations. Molecular design software and Comparison of nucleic acid simulation software are computational chemistry software, molecular dynamics software and molecular modelling software.

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Comparison of software for molecular mechanics modeling

This is a list of computer programs that are predominantly used for molecular mechanics calculations. Molecular design software and Comparison of software for molecular mechanics modeling are computational chemistry software, molecular dynamics software, molecular modelling software and science software.

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Discovery Studio

Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. Molecular design software and Discovery Studio are computational chemistry software and science software.

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DOCK

The program UCSF DOCK was created in the 1980s by Irwin "Tack" Kuntz's Group, and was the first docking program. Molecular design software and DOCK are molecular modelling software.

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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.

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Firefly (computer program)

Firefly, formerly named PC GAMESS, is an ab initio computational chemistry program for Intel-compatible x86, x86-64 processors based on GAMESS (US) sources. Molecular design software and Firefly (computer program) are computational chemistry software.

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FoldX

FoldX is a protein design algorithm that uses an empirical force field. Molecular design software and FoldX are molecular modelling software.

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Force field (chemistry)

In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms (or collections of atoms) within molecules or between molecules as well as in crystals.

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Freeware

Freeware is software, most often proprietary, that is distributed at no monetary cost to the end user.

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Lead Finder

Lead Finder is a computational chemistry tool designed for modelling protein-ligand interactions. Molecular design software and Lead Finder are molecular modelling software.

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List of molecular graphics systems

This is a list of notable software systems that are used for visualizing macromolecules.

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List of quantum chemistry and solid-state physics software

Quantum chemistry computer programs are used in computational chemistry to implement the methods of quantum chemistry. Molecular design software and List of quantum chemistry and solid-state physics software are computational chemistry software and molecular modelling software.

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List of software for Monte Carlo molecular modeling

This is a list of computer programs that use Monte Carlo methods for molecular modeling. Molecular design software and list of software for Monte Carlo molecular modeling are molecular modelling software.

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List of software for nanostructures modeling

This is a list of computer programs that are used to model nanostructures at the levels of classical mechanics and quantum mechanics. Molecular design software and list of software for nanostructures modeling are molecular modelling software.

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Materials Studio

Materials Studio is software for simulating and modeling materials. Molecular design software and materials Studio are computational chemistry software.

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Mathematical optimization

Mathematical optimization (alternatively spelled optimisation) or mathematical programming is the selection of a best element, with regard to some criteria, from some set of available alternatives.

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Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules.

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Molecular graphics

Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation.

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Molecular mechanics

Molecular mechanics uses classical mechanics to model molecular systems.

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Molecular model

A molecular model is a physical model of an atomistic system that represents molecules and their processes.

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Molecular modeling on GPUs

Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.

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Molecular modelling

Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules.

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Molecular Operating Environment

Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. Molecular design software and Molecular Operating Environment are computational chemistry software and molecular modelling software.

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Molecule editor

A molecule editor is a computer program for creating and modifying representations of chemical structures.

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OPLS

The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof.

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Partial charge

In atomic physics, a partial charge (or net atomic charge) is a non-integer charge value when measured in elementary charge units.

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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.

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Quantitative structure–activity relationship

Quantitative structure–activity relationship models (QSAR models) are regression or classification models used in the chemical and biological sciences and engineering.

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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 to physical and chemical properties of molecules, materials, and solutions at the atomic level.

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Quantum mechanics

Quantum mechanics is a fundamental theory that describes the behavior of nature at and below the scale of atoms.

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Rosetta@home

Rosetta@home is a volunteer computing project researching protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker lab.

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SAMSON

SAMSON (Software for Adaptive Modeling and Simulation Of Nanosystems) is a computer software platform for molecular design being developed by and previously by the NANO-D group at the French Institute for Research in Computer Science and Automation (INRIA). Molecular design software and SAMSON are computational chemistry software.

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Schrödinger, Inc.

Schrödinger, Inc. is an international scientific software company that specializes in developing computational tools and software for drug discovery and materials science. Molecular design software and Schrödinger, Inc. are molecular modelling software.

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Scigress

Scigress, stylised SCiGRESS, is a software suite designed for molecular modeling, computational and experimental chemistry, drug design, and materials science. Molecular design software and Scigress are computational chemistry software and molecular modelling software.

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References

[1] https://en.wikipedia.org/wiki/Molecular_design_software

Also known as Comparison of molecular design software.

Molecular design software, the Glossary

Table of Contents

See also

Molecular dynamics software

References