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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. See also *Car–Parrinello molecular dynamics *Comparison of force-field implementations *Comparison of nucleic acid simulation software *List of molecular graphics systems *List of protein structure prediction software *List of quantum chemistry and solid-state physics software * List of software for Monte Carlo molecular modeling * List of software for nanostructures modeling *Molecular design software *Molecular dynamics *Molecular modeling on GPUs *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 ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' representation in which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2008 report by the Standish Group stated that adoption of open-source software models has resulted in savings of about $60 billion per year for consumers. Open source code can be used for studying and allows capable end users to adapt software to their personal needs in a similar way user scripts an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FoldX
FoldX is a protein design algorithm that uses an empirical force field. It can determine the energetic effect of point mutations as well as the interaction energy of protein complexes (including Protein- DNA). FoldX can mutate protein and DNA side chains using a probability-based rotamer library, while exploring alternative conformations of the surrounding side chains. Applications * Prediction of the effect of point mutations or human SNPs on protein stability or protein complexes * Protein design to improve stability or modify affinity or specificity * Homology modeling The FoldX force field The energy function includes terms that have been found to be important for protein stability, where the energy of unfolding (∆G) of a target protein is calculated using the equation: ∆G = ∆Gvdw + ∆GsolvH + ∆GsolvP + ∆Ghbond + ∆Gwb + ∆Gel + ∆Smc + ∆Ssc Where ∆Gvdw is the sum of the Van der Waals contributions of all atoms with respect to the same interaction ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Foldit
Foldit is an online puzzle video game about protein folding. It is part of an experimental research project developed by the University of Washington, Center for Game Science, in collaboration with the UW Department of Biochemistry. The objective of Foldit is to fold the structures of selected proteins as perfectly as possible, using tools provided in the game. The highest scoring solutions are analyzed by researchers, who determine whether or not there is a native structural configuration (native state) that can be applied to relevant proteins in the real world. Scientists can then use these solutions to target and eradicate diseases and create biological innovations. A 2010 paper in the science journal ''Nature'' credited Foldit's 57,000 players with providing useful results that matched or outperformed algorithmically computed solutions. History Rosetta Prof. David Baker, a protein research scientist at the University of Washington, founded the Foldit project. Seth Cooper ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Discovery Studio
Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed bDassault Systemes BIOVIA(formerly Accelrys). The product suite has a stronacademic collaboration programme supporting scientific research and makes use of a number of software algorithms developed originally in the scientific community, including CHARMM, MODELLER, DELPHI, ZDOCK, DMol3 and more. Scope Discovery Studio provides software applications covering the following areas: * Simulations ** Including Molecular Mechanics, Molecular Dynamics, Quantum Mechanics ** 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 * Structure-based Design ** Inclu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Desmond (software)
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. The code uses novel parallel algorithms and numerical methods to achieve high performance on platforms containing multiple processors, but may also be executed on a single computer. The core and source code are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the Folding@home distributed computing project. Desmond is available as commercial software through Schrödinger, Inc. Molecular dynamics program Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle mesh Ewald-based methods. Constraints can be enforced using the M-SHAKE algorithm. These methods can be used together with time-scale splitting (RESPA-based) inte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CP2K
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical ( AM1, PM3, MNDO, MNDOd, PM6) and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition sta ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CHEMKIN
CHEMKIN is a proprietary software tool for solving complex chemical kinetics problems. It is used worldwide in the combustion, chemical processing, microelectronics and automotive industries, and also in atmospheric science. It was originally developed at Sandia National Laboratories and is now developed by a US company, Reaction Design. CHEMKIN solves thousands of reaction combinations to develop a comprehensive understanding of a particular process, which might involve multiple chemical species, concentration ranges, and gas temperatures. Chemical kinetics simulation software allows for a more time-efficient investigation of a potential new process compared to direct laboratory investigation. One important driver for the development and use of CHEMKIN is the reduction of pollutants, such as NOx. As these pollutants become more tightly regulated through agreements by agencies such as the United States Environmental Protection Agency and the California Air Resource Board (CARB ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BIOVIA
BIOVIA is a software company headquartered in the United States, with representation in Europe and Asia. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries. Previously named Accelrys, it is a wholly owned subsidiary of Dassault Systèmes after an April 2014 acquisition and has been renamed BIOVIA. History Accelrys was formed in 2001 as a wholly owned subsidiary of Pharmacopeia, Inc. from the fusion of five companies: Molecular Simulations Inc., Synopsys Scientific Systems, Oxford Molecular, the Genetics Computer Group (GCG), and Synomics Ltd. MSI, itself a result of the combination of Biodesign, Cambridge Molecular Design, Polygen and, later, Biocad and Biosym Technologies. In late 2003, Pharmacopeia, Inc. separated its drug discovery and software development businesses. The drug discovery company retained the name Pharmacopeia and remained in Princeton ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia. Force fields The CHARMM force fields for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19, all-atom CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF. In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OPLS
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University. Functional form The functional form of the OPLS force field is very similar to that of AMBER: E \left(r^N \right ) = E_\mathrm + E_\mathrm + E_\mathrm + E_\mathrm E_\mathrm = \sum_\mathrm K_r (r-r_0)^2 \, E_\mathrm = \sum_\mathrm k_\theta (\theta-\theta_0)^2 \, E_\mathrm = \sum_\mathrm \left( \frac \left 1 + \cos (\phi-\phi_1) \right + \frac \left 1 - \cos (2\phi-\phi_2) \right + \frac \left 1 + \cos (3\phi-\phi_3) \right + \frac \left 1 - \cos (4\phi-\phi_4) \right \right) E_\mathrm = \sum_ f_ \left( \frac - \frac + \frac \right) with the combining rules A_ = \sqrt and C_ = \sqrt. Intramolecular nonbonded interactions E_\mathrm are counted only for atoms three or more bonds apart; 1,4 interactions are sca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
