The pDynamo molecular modeling and simulation program
☆47Nov 24, 2025Updated 3 months ago
Alternatives and similar repositories for pDynamo3
Users that are interested in pDynamo3 are comparing it to the libraries listed below
Sorting:
- Automated Transition States Builder☆11Jun 1, 2023Updated 2 years ago
- FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook☆19Jun 10, 2023Updated 2 years ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Oct 2, 2024Updated last year
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 8 months ago
- A thermal rate constant calculator and kinetics Monte Carlo Simulator☆17Apr 12, 2024Updated last year
- Tool to compute bond and angle force field parameters with the Seminario method☆14Apr 15, 2018Updated 7 years ago
- Yasara Plugin for QM calculations☆14May 9, 2024Updated last year
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Jan 23, 2024Updated 2 years ago
- ☆12Jul 31, 2020Updated 5 years ago
- the simple alchemistry library☆235Jan 23, 2026Updated last month
- The core part of Atomic Charge Calculator III.☆29Updated this week
- Command line tool providing BOSS generated OPLS-AA/CM1A(-LBCC) parameters for organic molecules and ligands.☆11Oct 5, 2017Updated 8 years ago
- Molecular Orbital PACkage☆169Feb 21, 2026Updated last month
- TSCoDe is a systematical conformational embedder for small molecules. It helps computational chemists build transition states and binding…☆13Jan 6, 2025Updated last year
- Fork of library used in reading xtc files from GROMACS simulations☆14Mar 9, 2017Updated 9 years ago
- QUICK: A GPU-enabled ab intio quantum chemistry software package☆199Updated this week
- code and source data for de novo design of Kemp elimination paper☆24Sep 18, 2025Updated 6 months ago
- Flexible Artificial Intelligence Docking☆18Aug 27, 2025Updated 6 months ago
- Molden2AIM is a utility program which can be used to create AIM-WFN, AIM-WFX, and NBO-47 files from a Molden file.☆59Jul 17, 2025Updated 8 months ago
- ☆25Feb 28, 2023Updated 3 years ago
- An interoperable Python framework for biomolecular simulation.☆147Updated this week
- A repository containing the build steps for the ccpbiosim workshop on QM/MM☆68Mar 12, 2026Updated last week
- An engine for electrostatic ML embedding for multiscale modelling.☆27Mar 11, 2026Updated last week
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Aug 11, 2023Updated 2 years ago
- CREST - A program for the automated exploration of low-energy molecular chemical space.☆301Dec 9, 2025Updated 3 months ago
- mmCIF Core Access Library☆50Updated this week
- Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.☆75Mar 27, 2025Updated 11 months ago
- Mirror of pDynamo computational chemistry software, which does not currently use a public version control repository☆10Feb 23, 2017Updated 9 years ago
- The official implementation of Energy-Inspired Molecular Conformation Optimization (ICLR 2022)☆36Oct 15, 2022Updated 3 years ago
- Light-weight tight-binding framework☆190Dec 17, 2025Updated 3 months ago
- automated reaction profile generation☆199Mar 10, 2026Updated last week
- Protein discovery tool for mining in the Alphafold database based on the position of few amino acids.☆29Jan 16, 2026Updated 2 months ago
- Calculation of interatomic interactions in molecular structures☆123Sep 3, 2024Updated last year
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 11, 2026Updated last week
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated last year
- SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction☆232Sep 29, 2025Updated 5 months ago
- Pembrolizumab-like Antibody Hallucination using AlphaFold2☆15Nov 10, 2023Updated 2 years ago
- A deep reinforcement learning library for conformer generation.☆20Apr 15, 2024Updated last year
- Python API for the extended tight binding program package☆124Sep 3, 2024Updated last year