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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 softw ... [...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 mech ... [...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, and is being further developed commercially by Schrödinger, Inc. 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Freeware
Freeware is software, 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 the same process as ''shareware''. As s ... [...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 Universi ... [...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, thermochemical recipes including G3(MP2) and T1, and machine learning models like corrected MMFF and Est. Density Functional. 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, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scigress
Scigress, stylised SCiGRESS, is a software suite designed for molecular modeling, computational and experimental chemistry, drug design, and materials science. It is a successor to the ''Computer Aided Chemistry'' (CAChe) software and has been used to perform experiments on hazardous or novel biomolecules and proteins ''in silico''. Functions and use cases * Molecule editing. * Theory levels: DFT, semi-empirical, molecular mechanics and dynamics. * Determination of low energy conformations and thermodynamic properties. * Calculation and 3D visualization of electronic properties, such as partial charges, orbitals, electron densities, and electrostatic surfaces. * Analysis of transition states and intrinsic reaction coordinates. * Infrared, UV, and NMR Nuclear magnetic resonance (NMR) is a physical phenomenon in which atomic nucleus, nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near and far field, near field) and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SAMSON
SAMSON (Software for Adaptive Modeling and Simulation Of Nanosystems) is a computer software platform for molecular design being developed bOneAngstromand previously by the NANO-D group at the French Institute for Research in Computer Science and Automation (INRIA). SAMSON has a modular architecture that makes it suitable for different domains of nanoscience, including material science, life science, and drug design. SAMSON Elements SAMSON Elements are modules for SAMSON, developed with the SAMSON software development kit (SDK). SAMSON Elements help users perform tasks in SAMSON, including building new models, performing calculations, running interactive or offline simulations, and visualizing and interpreting results. SAMSON Elements may contain different class types, including for example: * ''Apps'' – generic classes with a graphical user interface that extend the functions of SAMSON * ''Editors'' – classes that receive user interaction events to provide editing functi ... [...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 lead discovery, fragment-based design, ligand-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, structural biology and bioinformatics, protein and antibody modeling, Molecular modelling, molecular modeling and simulations, virtual screening, Cheminformatics toolkits, cheminformatics & QSAR. The Scientific Vector Language (Scientific Vector Language, SVL) is the built-in command, scripting and application development language of MOE. History The Molecular Operating Environment was de ... [...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 interpretation o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lead Finder
Lead Finder is a computational chemistry tool designed for modelling protein-ligand interactions. It is used for conducting molecular docking studies and quantitatively assessing ligand binding and biological activity. It offers free access to users in commercial, academic, or other settings. About The original docking algorithm integrated into Lead Finder can be tailored for either quick but less accurate virtual screening applications or slower but more in-depth analyses. Lead Finder is used by computational and medicinal chemists for drug discovery, as well as pharmacologists and toxicologists involved in in silico In biology and other experimental sciences, an ''in silico'' experiment is one performed on a computer or via computer simulation software. The phrase is pseudo-Latin for 'in silicon' (correct ), referring to silicon in computer chips. It was c ... assessment of ADME-Tox properties. Additionally, it is used by biochemists and enzymologists working on modellin ... [...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 intera ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
