biomolecular-simulation

There are 1 repository under biomolecular-simulation topic.

TinkerTools / tinker
Tinker: Software Tools for Molecular Design
molecular-dynamics molecular-mechanics force-fields biomolecular-simulation molecular-modeling
Language:Fortran 124
michellab / BioSimSpace
Code and resources for the EPSRC BioSimSpace project.
biomolecular-simulation interoperability ccpbiosim computational-chemistry computational-physics computational-biology molecular-dynamics reproducibility reproducible-research
Language:Python 76
biosimspace
OpenBioSim / biosimspace
An interoperable Python framework for biomolecular simulation.
computational-biology computational-chemistry computational-physics drug-discovery interoperability molecular-dynamics reproducibility reproducible-research molecular-simulation biomolecular-simulation free-energy-calculations
Language:Python 62
TinkerTools / tinker9
Tinker9: Next Generation of Tinker with GPU Support
molecular-dynamics molecular-mechanics force-fields biomolecular-simulation molecular-modeling gpu-computing
Language:C++ 48
sire
OpenBioSim / sire
Sire Molecular Simulations Framework
biomolecular-simulation cplusplus molecular-simulation python free-energy-calculations
Language:C++ 35
delemottelab / demystifying
biomolecular-simulation deep-taylor-decomposition machine-learning molecular-dynamics
Language:Python 19
evanseitz / cryoEM_synthetic_generation
Simulation of cryo-EM ensemble data from atomic models of molecules exhibiting continuous motions
cryo-em biomolecular-simulation quantitative-biology ground-truth
Language:Python 12
sarisabban / Pose
A bare metal Python library for building and manipulating protein molecular structures
amino-acids bioinformatics biomolecular-simulation biomolecule computational-biology denovo denovo-design game-engine molecular-simulation molecule numpy pdb pose protein protein-design protein-structure proteins python topology
Language:Python 11
floWneffetS / tutorial_dcTMD
Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
nonequilibrium-thermodynamics nonequilibrium-physics free-energy friction tutorial physics-simulation biomolecular-simulation
Language:Python 7
PSDI-UK / aiida-gromacs
A GROMACS plugin for AiiDA
aiida-plugin biomolecular-simulation psdi-pf4
Language:Python 5
WagAd22 / ABC-Laboratory
ABC-Laboratory is a prototypical simulation software calculating the fluorescence or absorption of different 'biomolecules'. It uses the Godot Game Engive (v.3) and is the result of my Bachelor Hands-on / internship.
biochemistry chemistry biology bioinformatics laboratory laboratory-exercises fluorescence absorption biomolecule biomolecular-simulation simulation godot godot-game-engine godot-engine
Language:GDScript 2
achattaraj / Ksp_phase_separation
Tools for data generation and data analysis for the eLife research article - "The solubility product extends the buffering concept to heterotypic biomolecular condensates"
biophysics computational-biology stochastic-simulations biomolecular-simulation bionetgen springsalad
Language:Python 1
floWneffetS / dcTMD_scripts_v1.0
Python scripts for the application of dissipation-corrected targeted molecular dynamics analysis.
physics-simulation biomolecular-simulation free-energy-calculations friction coarse-graining nonequilibrium-physics nonequilibrium-thermodynamics
Language:Python 1
pomeslab / SharedCode
A collection of scripts and software to assist with biomolecular simulation in our laboratory
high-performance-computing gromacs biomolecular-simulation molecular-dynamics
Language:Shell 1
sarisabban / MiraMar
De novo cyclic protein polypeptide design using reinforcement learning.
biomolecular-simulation cleanrl computational-biology denovo-design game game-development games gym gym-environment machine-learning molecular-simulation numpy openai openai-gym protein-structure proteins reinforcement-learning scipy structural-biology tianshou
Language:Python 1
mazenahmad / RPCA
Relative Principle Components Analysis (RPCA)
conformational-changes biomolecular-simulation latent-variable-models representation-learning free-energy-calculations
Language:C 0
PSDI-UK / aiida-amber
An Amber plugin for AiiDA
aiida-plugin biomolecular-simulation psdi-pf4
Language:Python 0