Alternatives and similar repositories for LSDMap-DM-d-MD

Users that are interested in LSDMap-DM-d-MD are comparing it to the libraries listed below

• markovmodel / graphtime
  Encoding of transition probabilities with undirected graphical models
  ☆9Updated 6 years ago
• markovmodel / mdshare
  Get access to our MD data files.
  ☆28Updated last year
• DSIMB / MEDUSA
  A Deep Learning based protein flexibility prediction tool.
  ☆9Updated 2 years ago
• flatironinstitute / Ensemble-reweighting-using-Cryo-EM-particles
  ☆11Updated 11 months ago
• vuqv / cosmo
  COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM
  ☆12Updated last year
• markovmodel / pytram
  The pytram package is deprecated and no longer supported. We recommend to switch to PyEMMA
  ☆9Updated 8 years ago
• bowman-lab / enspara
  Modeling molecular ensembles with scalable data structures and parallel computing
  ☆34Updated 3 months ago
• PatWalters / metk
  Model Evaluation Toolkit
  ☆27Updated 6 years ago
• noinil / genesis_cg_tool
  Prepare topology and coordinate file for CG models in Genesis.
  ☆11Updated 7 months ago
• markovmodel / adaptivemd
  A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
  ☆18Updated last year
• markovmodel / ivampnets
  ☆25Updated 2 years ago
• markovmodel / pyemma_tutorials
  How to analyze molecular dynamics data with PyEMMA
  ☆75Updated 5 years ago
• julie-forman-kay-lab / IDPConformerGenerator
  Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space
  ☆23Updated 2 months ago
• xuhuihuang / graphvampnets
  GraphVAMPnets combines graph neural networks with variational approach for Markovian process (VAMP) theory to identify the slow collectiv…
  ☆11Updated last year
• Ferg-Lab / DiAMoNDBack
  DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces
  ☆19Updated this week
• openmm / openmmexampleplugin
  An example of how to write a plugin for OpenMM
  ☆31Updated last year
• KULL-Centre / FRETpredict
  Software for the prediction of FRET data from conformational ensembles.
  ☆23Updated 4 months ago
• noegroup / reform
  A simple implementation of replica exchange MD simulations for OpenMM.
  ☆23Updated 3 years ago
• tiwarylab / SGOOP
  Spectral Gap Optimization of Parameters
  ☆17Updated 5 years ago
• bio-phys / PyDHAMed
  Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
  ☆20Updated 7 years ago
• BrooksResearchGroup-UM / FastMBAR
  A fast solver for large scale MBAR/UWHAM equations
  ☆39Updated 8 months ago
• jhenin / qwrap
  Fast PBC wrapping and unwrapping for VMD
  ☆23Updated 5 months ago
• ExcitedStates / qfit-3.0
  qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.
  ☆41Updated last week
• greener-group / GB99dms
  The GB99dms implicit solvent force field for proteins, plus scripts and data
  ☆22Updated last year
• MobleyLab / blues
  Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
  ☆33Updated last month
• MobleyLab / benchmarksets
  Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
  ☆42Updated 3 years ago
• andrrizzi / tfep-revisited-2021
  Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped refe…
  ☆13Updated 3 years ago
• openmm / openmm-xtb
  OpenMM plugin to interface with XTB
  ☆16Updated 2 months ago
• luigibonati / deep-learning-slow-modes
  Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"
  ☆20Updated 11 months ago
• DEShawResearch / sns-mp2
  ☆27Updated 4 years ago