Alternatives and similar repositories for PathDetect-SOM

Users that are interested in PathDetect-SOM are comparing it to the libraries listed below

• forlilab / cosolvkit
  CosolvKit is a versatile tool for cosolvent MD preparation and analysis
  ☆28Updated 2 months ago
• Gervasiolab / OpenBPMD
  ☆68Updated 2 years ago
• bigginlab / ABFE_workflow
  This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
  ☆58Updated last week
• GHeinzelmann / GHOAT.py
  The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.
  ☆21Updated 7 months ago
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆18Updated 2 months ago
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆34Updated 2 years ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆24Updated 3 years ago
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆34Updated 3 months ago
• keisuke-yanagisawa / exprorer
  EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation
  ☆11Updated 3 years ago
• tubiana / screening_protocol
  Screening protocol with AUTODOCK-GPU
  ☆14Updated 2 years ago
• freeenergylab / FEP-SPell-ABFE
  FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery
  ☆78Updated 11 months ago
• IFMlab / ChemFlow
  Computational Chemistry Workflows
  ☆56Updated 3 years ago
• callumjd / AMBER-Umbrella_COM_restraint_tutorial
  Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
  ☆39Updated 2 years ago
• HITS-MCM / tauRAMD
  Computation of the drug-target relative residence times from RAMD simulations
  ☆20Updated last year
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆31Updated 2 months ago
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆39Updated 2 years ago
• limresgrp / FMAP_v1
  Codes to use funnel-metadynamics and funnel metadynamics automated protocol
  ☆30Updated 4 years ago
• rinikerlab / reeds
  This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…
  ☆32Updated 6 months ago
• dlukauskis / funnel_maker
  Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.
  ☆15Updated 2 years ago
• otayfuroglu / deepQM
  ☆28Updated 7 months ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• ci-lab-cz / streamd
  Fully automated high-throughput MD pipeline
  ☆86Updated last week
• Gervasiolab / Gervasio-Protein-Dynamics
  A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery
  ☆13Updated 9 months ago
• giaguaro / PROTACable
  PROTACable is an end-to-end in-silico design toolkit for novel PROTACs
  ☆29Updated last year
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆22Updated 2 months ago
• mqcomplab / PRIME
  protein structure prediction with precision
  ☆26Updated last year
• HITS-MCM / gromacs-ramd
  Random Acceleration Molecular Dynamics in GROMACS
  ☆42Updated last year
• netscianalysis / netsci
  ☆14Updated last year
• pablo-arantes / ParametrizANI
  Free Parametrization for Small Molecules
  ☆49Updated 2 months ago
• protocaller / ProtoCaller
  Full automation of relative protein-ligand binding free energy calculations in GROMACS
  ☆46Updated 4 years ago