dkoes / md-scripts

Related projects ⓘ

Alternatives and complementary repositories for md-scripts

• protocaller / ProtoCaller
  Full automation of relative protein-ligand binding free energy calculations in GROMACS
  ☆43Updated 3 years ago
• IFMlab / ChemFlow
  Computational Chemistry Workflows
  ☆53Updated 2 years ago
• michellab / BioSimSpaceTutorials
  ☆25Updated 10 months ago
• JoaoRodrigues / openmm_scripts
  Collection of Python scripts to setup and run simulations with OpenMM
  ☆14Updated 4 years ago
• kamerlinlab / KIF
  KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
  ☆23Updated 5 months ago
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆32Updated 11 months ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆22Updated last year
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆37Updated last year
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆22Updated 3 months ago
• rinikerlab / restraintmaker
  Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…
  ☆17Updated 2 years ago
• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆34Updated last year
• arwalkerlab / AutoParams
  ☆26Updated 10 months ago
• otayfuroglu / deepQM
  ☆27Updated 5 months ago
• openmm / openmm_workshops
  ☆32Updated 2 months ago
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆10Updated 2 years ago
• ChemBioHTP / EnzyHTP
  EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling
  ☆13Updated this week
• ci-lab-cz / streamd
  Automate MD associated calculations
  ☆35Updated this week
• schrodinger / public_binding_free_energy_benchmark
  The public versio
  ☆36Updated last year
• mobiochem / MoBioTools
  A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…
  ☆27Updated 9 months ago
• ParImmune / SINAPs
  ☆18Updated 3 years ago
• 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.
  ☆12Updated 3 months ago
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆27Updated 4 months ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆18Updated 2 years ago
• MiaoLab20 / pyreweighting
  ☆25Updated last year
• ci-lab-cz / easydock
  ☆37Updated 3 months ago
• mahendra-awale / medchem_moves
  ☆44Updated 4 years 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.
  ☆13Updated last year
• wolberlab / dynophores
  Dynamic pharmacophore modeling of molecular interactions
  ☆31Updated 6 months ago
• BrooksResearchGroup-UM / pyCHARMM-Workshop
  pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…
  ☆63Updated last year
• seekrcentral / seekr2
  Simulation-Enabled Estimation of Kinetic Rates - Version 2
  ☆27Updated 3 weeks ago