Alternatives and similar repositories for pdb2oniom

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

• shirtsgroup / cg_openmm
  Tools to build coarse grained models and perform simulations with OpenMM
  ☆24Updated 2 years ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆22Updated 2 years ago
• chonglab-pitt / wedap
  Weighted Ensemble Data Analysis and Plotting
  ☆24Updated 8 months ago
• MiaoLab20 / pyreweighting
  ☆28Updated last year
• ParImmune / SINAPs
  ☆18Updated 3 years ago
• federico-fogolari / pdb2entropy
  Entropy from PDB conformational ensembles
  ☆8Updated last year
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆16Updated 2 years ago
• masoudk / AsiteDesign
  ☆13Updated last year
• kamerlinlab / KIF
  KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
  ☆29Updated last week
• kamerlinlab / KIN
  Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…
  ☆17Updated last year
• visvaldask / gmx_makecyclictop
  This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…
  ☆13Updated 4 years ago
• keisuke-yanagisawa / exprorer_msmd
  MSMD (mixed-solvent molecular dynamics) engine and analysis tools
  ☆19Updated 2 months ago
• ELELAB / PDBminer
  scripts to find PBD structures for cancer driver proteins
  ☆31Updated 3 months ago
• bussilab / MDRefine
  ☆16Updated 3 weeks ago
• molecularmodelingsection / TTMD
  Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations
  ☆19Updated 8 months ago
• KULL-Centre / DEERpredict
  Software for the prediction of DEER and PRE data from conformational ensembles.
  ☆12Updated last month
• Exscientia / plif_validity
  Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"
  ☆16Updated 8 months ago
• quantaosun / Pymol_Script
  A python script for PyMol to make protein-ligand interaction images.
  ☆11Updated 2 months ago
• Hoecker-Lab / pocketoptimizer
  Binding pocket optimization based on force fields and docking scoring functions
  ☆33Updated 2 months ago
• oxpig / AEV-PLIG
  ☆21Updated 3 months ago
• plinder-org / runs-n-poses
  A benchmark dataset for protein-ligand co-folding prediction
  ☆20Updated 3 months ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• LongxingCao / pymol_scripts
  bakerlab pymol scripts
  ☆23Updated 5 years ago
• darrenjhsu / tiny_IFD
  Lightweight induced fit docking
  ☆21Updated 2 years ago
• ci-lab-cz / streamd
  Fully automated high-throughput MD pipeline
  ☆60Updated 3 weeks ago
• delemottelab / allosteric-pathways
  Building and analyzing residue interaction networks with cofactors (includes tutorial).
  ☆17Updated 4 years ago
• mqcomplab / PRIME
  protein structure prediction with precision
  ☆18Updated last year
• GilbertoPPereira / PROTACability
  ☆12Updated last year
• ld139 / ApoDock_public
  Code for ApoDock
  ☆20Updated 2 months ago
• JingHuangLab / openmm_deepmd_plugin
  ☆22Updated 2 weeks ago