Alternatives and similar repositories for pdb2oniom

Users that are interested in pdb2oniom are comparing it to the libraries listed below

• pablo-arantes / ParametrizANI
  Free Parametrization for Small Molecules
  ☆49Updated 2 months ago
• shirtsgroup / cg_openmm
  Tools to build coarse grained models and perform simulations with OpenMM
  ☆24Updated 2 years ago
• chonglab-pitt / wedap
  Weighted Ensemble Data Analysis and Plotting
  ☆24Updated 5 months ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆24Updated 3 years ago
• kamerlinlab / KIF
  KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
  ☆32Updated last month
• ParImmune / SINAPs
  ☆18Updated 4 years ago
• bioexcel / cp2K_qmmm_tutorials_for_biological_simulations
  Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
  ☆22Updated 6 years ago
• dkoes / md-scripts
  A collections of scripts for working molecular dynamics simulations
  ☆44Updated 4 months ago
• MiaoLab20 / pyreweighting
  ☆32Updated 2 years ago
• maxscheurer / pycontact
  Analysis of non-covalent interactions in MD trajectories
  ☆65Updated 11 months ago
• GoMartini3-tools / Native-contacts-determination-from-MD
  We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…
  ☆16Updated last year
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆18Updated 2 months ago
• 9527567 / AmberMDrun
  ☆16Updated last year
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆31Updated last month
• wolberlab / mdpath
  MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral ang…
  ☆26Updated last month
• bussilab / MDRefine
  ☆16Updated 3 months ago
• choderalab / kinase-metadynamics
  To run metadynamics simulations using openMM (based on Peter Eastman's script)
  ☆13Updated 6 years ago
• ZhuofanShen / Rosetta-Enzyme-Design-Pipeline
  ☆10Updated 3 weeks ago
• keisuke-yanagisawa / exprorer_msmd
  MSMD (mixed-solvent molecular dynamics) engine and analysis tools
  ☆19Updated 8 months ago
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆18Updated 2 years ago
• markusfleck / PARENT
  PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems
  ☆16Updated 3 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.
  ☆15Updated 2 years ago
• kzinovjev / string-amber
  Adaptive string method implementation in AmberTools23 and Amber22
  ☆13Updated 11 months 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.
  ☆21Updated 6 months ago
• visvaldask / gmx_makecyclictop
  This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…
  ☆14Updated 5 years ago
• ci-lab-cz / streamd
  Fully automated high-throughput MD pipeline
  ☆85Updated 3 months ago
• ksy141 / mstool
  Multiscale Simulation Tool for Backmapping
  ☆21Updated 2 months ago
• delemottelab / allosteric-pathways
  Building and analyzing residue interaction networks with cofactors (includes tutorial).
  ☆17Updated 4 years ago
• jhenin / SAFEP_tutorial
  A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
  ☆15Updated 8 months ago
• GilbertoPPereira / PROTACability
  ☆12Updated 2 years ago