Recurrent Units-based Molecular Modeling
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Updated
Mar 26, 2019 - Python
Recurrent Units-based Molecular Modeling
Mirror of pDynamo computational chemistry library
Atoms In Molecules Neural Network Potential
Real time monitoring and visualization of Amber MD simulations
Use the MMLigner structural alignment program from within Yasara!
Моделирование системы Леннарда-Джонса в ячейке 10х10х10 атомов
(archived) A simple chemical structure graph modeling, drawing and analysis toolkit
UV-vis spectra simulation program from oscillator strength results.
Pip installable version of the encoder portion of the Junction Tree Variational Autoencoder https://arxiv.org/abs/1802.04364,
Git repo for the paper "Physics-constrained predictive molecular latent space discovery with graph scattering variational autoencoder."
GraSeq: Graph and Sequence Fusion Learning for Molecular Property Prediction. In CIKM 2020.
Force field parameters and supplementary scripts for the "A coarse-grained model for DNA origami" paper by R. Reshetnikov, A. Stolyarova, A. Zalevsky et. al.
Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.
This tool is designed to automate the process of protein modeling. To search for homologues in the Swiss-Model and wwPDB databases. Alignment is done using mufft with L-INS-i algorithm tool. Rosetta is used to model proteins. Ornate 3D is used to assess the quality of models
Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization
PyMOL plugin to modify molecular structure via turnstile rotation
Retrieve the molecules from the ChEBI site, and parse them and extract the information important for the execution of the Nauty mckay algorithm.
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