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JCMsuite – a finite element analysis software for simulating optical properties of nanostructures LAMMPS – Open source molecular dynamics code MAPS - Graphical user interface to build complex systems (nanostructures, polymers, surfaces...), set up and analyze ab-initio (Quantum Espresso, VASP, Abinit, NWChem...) or classical (LAMMPS, Towhee ...
List of software for Monte Carlo molecular modeling; Comparison of software for molecular mechanics modeling; Molecular design software; Molecule editor; Molecular modeling on GPUs; List of software for nanostructures modeling; Semi-empirical quantum chemistry method; Computational chemical methods in solid-state physics, with periodic boundary ...
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:
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Amira (ah-MEER-ah) is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo.
The software C++ library for LC-MS/MS data management and analysis offers an infrastructure for the development of mass spectrometry-related software. It allows peptide and metabolite quantification and supports label-free and isotopic-label-based quantification (such as iTRAQ and TMT and SILAC ) as well as targeted SWATH-MS quantification.
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
Modo was created by the same core group of software engineers that previously created the pioneering 3D application LightWave 3D, originally developed on the Amiga platform and bundled with the Amiga-based Video Toaster workstations that were popular in television studios in the late 1980s and early 1990s.