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High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
A molecular assembler is a kind of molecular machine. Some biological molecules such as ribosomes fit this definition. This is because they receive instructions from messenger RNA and then assemble specific sequences of amino acids to construct protein molecules. However, the term "molecular assembler" usually refers to theoretical human-made ...
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). [2] [3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed satisfaction of spatial restraints, by which a set of geometrical criteria are used to create a probability ...
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 ...
Molecular Operating Environment (MOE) HM MD MM NA QM SMI XRD: Proprietary: Windows, Linux, OS X; SVL programming language Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications ...
The authors make several suggestions for assembly: 1) use more than one assembler, 2) use more than one metric for evaluation, 3) select an assembler that excels in metrics of more interest (e.g., N50, coverage), 4) low N50s or assembly sizes may not be concerning, depending on user needs, and 5) assess the levels of heterozygosity in the ...
Space-filling model of loratadine created using Avogadro.. Molecule builder-editor for Windows, Linux, Unix, and macOS.; All source code is licensed under the GNU General Public License (GPL) version 2.
Spartan is a molecular modelling and computational chemistry application from Wavefunction. [2] It contains code for molecular mechanics, semi-empirical methods, ab initio models, [3] density functional models, [4] post-Hartree–Fock models, [5] thermochemical recipes including G3(MP2) [6] and T1.