Alternatives and similar repositories for upside2-md:

Users that are interested in upside2-md are comparing it to the libraries listed below

• sosnicklab / upside-md
  Coarse-grained molecular dynamics for protein physics. NOTE: this has been superseded by Upside 2: https://github.com/sosnicklab/upside2-…
  ☆23Updated 3 years ago
• huhlim / cg2all
  Convert coarse-grained protein structure to all-atom model
  ☆37Updated 10 months ago
• KULL-Centre / CALVADOS
  ☆57Updated last week
• tiwarylab / alphafold2rave
  ☆68Updated 9 months ago
• tommyhuangthu / FASPR
  an ultra-fast and accurate program for deterministic protein sidechain packing
  ☆30Updated last month
• maccallumlab / martini_openmm
  ☆54Updated last year
• KULL-Centre / _2024_Cao_CALVADOSCOM
  ☆16Updated 2 weeks ago
• BrooksResearchGroup-UM / pyCHARMM-Workshop
  pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…
  ☆69Updated 3 months ago
• ChemBioHTP / EnzyHTP
  EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling
  ☆20Updated this week
• paulrobustelli / Force-Fields
  Force Fields
  ☆57Updated 2 months ago
• fmaschietto / mdigest
  ☆31Updated 6 months ago
• bestlab / force_fields
  Force fields in various formats
  ☆26Updated 11 months ago
• maccallumlab / meld
  Modeling with limited data
  ☆57Updated 5 months ago
• Hekstra-Lab / SFcalculator
  ☆18Updated 3 months ago
• MiaoLab20 / gamd-openmm
  Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…
  ☆80Updated 10 months ago
• tdudgeon / simple-simulate-complex
  Simple protein-ligand complex simulation with OpenMM
  ☆83Updated last year
• tiwarylab / af2rave
  Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2
  ☆46Updated this week
• PKUGaoGroup / DSDP
  Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, …
  ☆57Updated 5 months ago
• HITS-MCM / gromacs-ramd
  Random Acceleration Molecular Dynamics in GROMACS
  ☆36Updated 9 months ago
• intbio / gromacs_ff
  Trusted force field files for gromacs
  ☆47Updated 5 months ago
• sulfierry / free_energy_landscape
  The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…
  ☆20Updated 2 months ago
• freesasa / freesasa-python
  FreeSASA Python Module
  ☆54Updated last year
• torchmd / torchmd-protein-thermodynamics
  Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
  ☆80Updated 2 months ago
• matteoferla / rdkit_to_params
  Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file
  ☆32Updated last year
• getcontacts / getcontacts
  Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation
  ☆111Updated last year
• fhh2626 / BFEE2
  binding free energy estimator 2
  ☆112Updated 4 months ago
• KULL-Centre / papers
  Material from papers from KULL centre
  ☆69Updated 10 months ago
• pstansfeld / MemProtMD
  ☆38Updated 3 weeks ago
• xuhuihuang / GME_tutorials
  Tutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.
  ☆23Updated 8 months ago
• CharlesHahn / DuIvy
  some scripts for analysis of MD and CADD. And some tutorials.
  ☆54Updated 8 months ago