Alternatives and similar repositories for Upside-MD

Users that are interested in Upside-MD are comparing it to the libraries listed below

• PDBeurope / arpeggio
  Calculation of interatomic interactions in molecular structures
  ☆107Updated last year
• KULL-Centre / CALVADOS
  ☆71Updated 3 months ago
• tommyhuangthu / FASPR
  Fast, accurate, and deterministic protein side-chain packing
  ☆36Updated 6 months ago
• bowman-lab / enspara
  Modeling molecular ensembles with scalable data structures and parallel computing
  ☆36Updated 2 months ago
• clauswilke / PeptideBuilder
  A simple Python library to generate model peptides
  ☆87Updated 4 years ago
• npschafer / openawsem
  An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM
  ☆37Updated 3 months ago
• samuelmurail / gromacs_py
  Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software. Gromacs_py can build topologie based on a…
  ☆49Updated 3 years ago
• KULL-Centre / BME
  Integrating Molecular Simulation and Experimental Data
  ☆24Updated 4 years ago
• maccallumlab / meld
  Modeling with limited data
  ☆59Updated 2 months ago
• freesasa / freesasa-python
  FreeSASA Python Module
  ☆56Updated last month
• dwhswenson / contact_map
  Contact map analysis for biomolecules; based on MDTraj
  ☆46Updated 9 months ago
• alchemistry / alchemical-best-practices
  Best practice document for alchemical free energy calculations going to livecoms journal
  ☆76Updated this week
• drorlab / pensa
  PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
  ☆144Updated 7 months ago
• ChemBioHTP / EnzyHTP
  EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling
  ☆27Updated last week
• biotite-dev / hydride
  Adding hydrogens to molecular models
  ☆48Updated this week
• delalamo / af2_conformations
  A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2
  ☆97Updated 2 years ago
• srnas / barnaba
  Analyse Nucleic Acids Structure and Simulations with baRNAba
  ☆45Updated last year
• tiwarylab / alphafold2rave
  ☆69Updated last year
• RashmiKumari / g_mmpbsa
  MM-PBSA method for GROMACS. For full description, please visit homepage:
  ☆67Updated 3 months ago
• PDBeurope / ccdutils
  A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dicti…
  ☆68Updated 3 weeks ago
• intbio / gromacs_ff
  Trusted force field files for gromacs
  ☆59Updated 10 months ago
• pstansfeld / MemProtMD
  ☆45Updated 4 months ago
• michellab / BioSimSpace
  Code and resources for the EPSRC BioSimSpace project.
  ☆78Updated 3 weeks ago
• dseeliger / pmx
  Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
  ☆65Updated 4 years ago
• michellab / Sire
  Sire Molecular Simulations Framework
  ☆96Updated 2 years ago
• PDBeurope / pdbecif
  A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB"
  ☆38Updated last year
• tekpinar / correlationplus
  A Python package to calculate, visualize and analyze correlation maps of proteins.
  ☆41Updated 3 weeks ago
• choderalab / openmm-tutorials
  Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM
  ☆49Updated 8 years ago
• mmtsb / toolset
  MMTSB Tool Set
  ☆32Updated last month
• Psivant / stormm
  STORMM: Structure and TOpology Replica Molecular Mechanics
  ☆80Updated 2 weeks ago