Alternatives and similar repositories for upside2-md

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

• KULL-Centre / CALVADOS
  ☆78Updated last month
• tiwarylab / alphafold2rave
  ☆69Updated last year
• huhlim / cg2all
  Convert coarse-grained protein structure to all-atom model
  ☆46Updated 5 months ago
• maccallumlab / martini_openmm
  ☆58Updated 2 years ago
• MiaoLab20 / gamd-openmm
  Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…
  ☆88Updated 4 months ago
• VTX-Molecular-Visualization / VTX
  ☆63Updated this week
• KULL-Centre / _2024_Cao_CALVADOSCOM
  ☆19Updated 7 months ago
• sosnicklab / upside-md
  Coarse-grained molecular dynamics for protein physics. NOTE: this has been superseded by Upside 2: https://github.com/sosnicklab/upside2-…
  ☆25Updated 3 years ago
• paulrobustelli / Force-Fields
  Force Fields
  ☆66Updated 9 months ago
• fmaschietto / mdigest
  ☆34Updated last year
• tommyhuangthu / FASPR
  Fast, accurate, and deterministic protein side-chain packing
  ☆36Updated 8 months ago
• tristanic / isolde
  Interactive molecular dynamics based model building into low-resolution crystallographic and cryo-EM maps
  ☆39Updated 3 months ago
• intbio / gromacs_ff
  Trusted force field files for gromacs
  ☆64Updated last year
• BrooksResearchGroup-UM / pyCHARMM-Workshop
  pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…
  ☆72Updated last month
• schrodinger / public_binding_free_energy_benchmark
  The public versio
  ☆67Updated 2 years ago
• ChemBioHTP / EnzyHTP
  EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling
  ☆29Updated this week
• Hekstra-Lab / SFcalculator
  ☆20Updated 4 months ago
• tdudgeon / simple-simulate-complex
  Simple protein-ligand complex simulation with OpenMM
  ☆91Updated 2 years ago
• CCPBioSim / qmmm-workshop
  A repository containing the build steps for the ccpbiosim workshop on QM/MM
  ☆68Updated this week
• maccallumlab / meld
  Modeling with limited data
  ☆59Updated 4 months ago
• giacomo-janson / idpsam
  Generate intrinsically disordered peptide conformations via machine learning
  ☆24Updated last year
• PDBeurope / arpeggio
  Calculation of interatomic interactions in molecular structures
  ☆112Updated last year
• getcontacts / getcontacts
  Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation
  ☆132Updated 2 years ago
• bestlab / force_fields
  Force fields in various formats
  ☆26Updated last year
• tiwarylab / af2rave
  Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2
  ☆59Updated last month
• pstansfeld / MemProtMD
  ☆45Updated this week
• bunzela / AIzymes
  ☆60Updated 3 weeks ago
• torchmd / torchmd-protein-thermodynamics
  Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
  ☆90Updated 9 months ago
• POVME / POVME3
  A pocket volume analyzer for use in protein modeling.
  ☆57Updated 3 years ago
• marrink-lab / vermouth-martinize
  Describe and apply transformation on molecular structures and topologies
  ☆127Updated 3 weeks ago