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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 chemistry, such software ''directly'' supports the aspects related to constructing molecular models, including: * Molecular graphics * interactive molecular drawing and conformational editing * building polymeric molecules, crystals, and solvated systems * partial charges 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 {{columns-list, colwidth=30em, *Molecule editor *Molecular modelling *Molecular modeling on GPUs *Protein design *Drug design *Force field (chemistry) *Comparison of force field implementations *Comparison of nucleic acid simulation software *Comparison of software for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical mec ... [...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] |
Freeware
Freeware is software, most often proprietary, that is distributed at no monetary cost to the end user. There is no agreed-upon set of rights, license, or EULA that defines ''freeware'' unambiguously; every publisher defines its own rules for the freeware it offers. For instance, modification, redistribution by third parties, and reverse engineering are permitted by some publishers but prohibited by others. Unlike with free and open-source software, which are also often distributed free of charge, the source code for freeware is typically not made available. Freeware may be intended to benefit its producer by, for example, encouraging sales of a more capable version, as in the freemium and shareware business models. History The term ''freeware'' was coined in 1982 by Andrew Fluegelman, who wanted to sell PC-Talk, the communications application he had created, outside of commercial distribution channels. Fluegelman distributed the program via a process now termed '' shareware''. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tinker (software)
Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means. Tinker works on Windows, macOS, Linux and Unix. The source code is available free of charge to non-commercial users under a proprietary license. The code is written in portable FORTRAN 77, Fortran 95 or CUDA with common extensions, and some C. Core developers are: (athe Jay Ponder lab at the Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri. Laboratory head Ponder is Full Professor of Chemistry, and of Biochemistry & Molecular Biophysics; (bthe Pengyu Ren lab at the Department of Biomedical Engineering Universit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Spartan (chemistry Software)
Spartan is a molecular modelling and computational chemistry application from Wavefunction. It contains code for molecular mechanics, semi-empirical methods, ''ab initio'' models, density functional models, post-Hartree–Fock models, and thermochemical recipes including G3(MP2) and T1. Quantum chemistry calculations in Spartan are powered by Q-Chem. Primary functions are to supply information about structures, relative stabilities and other properties of isolated molecules. Molecular mechanics calculations on complex molecules are common in the chemical community. Quantum chemical calculations, including Hartree–Fock method molecular orbital calculations, but especially calculations that include electronic correlation, are more time-consuming in comparison. Quantum chemical calculations are also called upon to furnish information about mechanisms and product distributions of chemical reactions, either directly by calculations on transition states, or based on Hammond's p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scigress
Scigress, stylized SCiGRESS, is a software suite for molecular modelling, computational chemistry, drug design, and materials science, a successor to ''Computer Aided Chemistry'' (CAChe) software. About Scigress is a molecular modeling suite for both experimental and computational chemists and biochemists. It enables researchers to study and design wide range of molecular systems: * organic * inorganic * polymers * proteins * metals, oxides, and ceramics Functions * Intuitive, easy to learn, property driven user interface including molecule editor and batch processing. * Theory levels: DFT, semi-empirical, molecular mechanics and dynamics. * Determination of low energy conformations and thermodynamic properties. * Calculare and 3D-visualize electronic properties: partial charges, orbitals, electron densities, and electrostatic surfaces and more. * Analysis of chemical reactions: transition states and intrinsic reaction coordinates. * Spectroscopic properties analysis: ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SAMSON
Samson (; , '' he, Šīmšōn, label= none'', "man of the sun") was the last of the judges of the ancient Israelites mentioned in the Book of Judges (chapters 13 to 16) and one of the last leaders who "judged" Israel before the institution of the monarchy. He is sometimes considered as an Israelite version of the popular Near Eastern folk hero also embodied by the Sumerian Enkidu and the Greek Heracles. The biblical account states that Samson was a Nazirite, and that he was given immense strength to aid him against his enemies and allow him to perform superhuman feats, including slaying a lion with his bare hands and massacring an entire army of Philistines using only the jawbone of a donkey. However, if Samson's long hair were cut, then his Nazirite vow would be violated and he would lose his strength. Samson is betrayed by his lover Delilah, who, sent by the Philistines officials to entice him, orders a servant to cut his hair while he is sleeping and turns him over to hi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 laboratory at the University of Washington. Rosetta@home aims to predict protein–protein docking and design new proteins with the help of about fifty-five thousand active volunteered computers processing at over 487,946 GigaFLOPS on average as of September 19, 2020. Foldit, a Rosetta@home videogame, aims to reach these goals with a crowdsourcing approach. Though much of the project is oriented toward basic research to improve the accuracy and robustness of proteomics methods, Rosetta@home also does applied research on malaria, Alzheimer's disease, and other pathologies. Like all BOINC projects, Rosetta@home uses idle computer processing resources from volunteers' computers to perform calculations on individual workunits. Completed results are sent to a central project server where they are validate ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and macOS. Main application areas in MOE include structure-based design, fragment-based design, ligand-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, structural biology and bioinformatics, protein and antibody modeling, molecular modeling and simulations, virtual screening, cheminformatics & QSAR. The Scientific Vector Language ( SVL) is the built-in command, scripting and application development language of MOE. History The Molecular Operating Environment was developed by the Chemical Computing Group under the supervision of President/CEO Paul Labute. Founded in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Materials Studio
Materials Studio is software for simulating and modeling materials. It is developed and distributed by BIOVIA (formerly Accelrys), a firm specializing in research software for computational chemistry, bioinformatics, cheminformatics, molecular dynamics simulation, and quantum mechanics. This software is used in advanced research of various materials, such as polymers, carbon nanotubes, catalysts, metals, ceramics, and so on, by universities (e.g., North Dakota State University), research centers, and high tech companies. Materials Studio is a client–server model software package with Microsoft Windows-based PC clients and Windows and Linux-based servers running on PCs, Linux IA-64 workstations (including Silicon Graphics (SGI) Altix) and HP XC clusters. Software components *Analytical and Crystallization: to investigate, predict, and modify crystal structure and crystal growth. **Morphology **Polymorph Predictor **Reflex, Reflex Plus, Reflex QPA: to assist the interpretat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lead Finder
Lead Finder software is a computational chemistry application for modeling protein-ligand interactions. The software can be used in molecular docking studies, for the quantitative evaluation of ligand binding and biological activity. For individual, non-commercial and academic users the software is free. About Lead Finder software is an integrated solution for simulating structure and binding affinity of protein-ligand complexes. The software combines automatic processing of protein structures, extra precision protein-ligand docking and calculation of free energy of ligand binding. Original docking algorithm provides a fast rate of calculations, which can be easily adjusted from more rapid (for virtual screening applications) to slightly more slow and robust, while unique scoring function implemented in Lead Finder provides unsurpassed accuracy of calculations. Lead Finder is intended to meet the requirements of computational and medicinal chemists involved in drug discovery, ph ... [...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] |
