The pDynamo molecular modeling and simulation program
☆49Nov 24, 2025Updated 8 months ago
Alternatives and similar repositories for pDynamo3
Users that are interested in pDynamo3 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Automated Transition States Builder☆11Jun 1, 2023Updated 3 years ago
- Yasara Plugin for QM calculations☆15Jul 26, 2026Updated 2 weeks ago
- FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook☆19Jun 10, 2023Updated 3 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 last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Tool to compute bond and angle force field parameters with the Seminario method☆14Apr 15, 2018Updated 8 years ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Jan 23, 2024Updated 2 years ago
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆126Updated this week
- The core part of Atomic Charge Calculator III.☆30Apr 30, 2026Updated 3 months ago
- the simple alchemistry library☆241Jun 1, 2026Updated 2 months ago
- ☆12Jul 31, 2020Updated 6 years ago
- Command line tool providing BOSS generated OPLS-AA/CM1A(-LBCC) parameters for organic molecules and ligands.☆11Oct 5, 2017Updated 8 years ago
- Light-weight tight-binding framework☆215Updated this week
- Molecular Orbital PACkage☆184Updated this week
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- A thermal rate constant calculator and kinetics Monte Carlo Simulator☆19Apr 12, 2024Updated 2 years ago
- TSCoDe is a systematical conformational embedder for small molecules. It helps computational chemists build transition states and binding…☆14Jan 6, 2025Updated last year
- Fork of library used in reading xtc files from GROMACS simulations☆14Mar 9, 2017Updated 9 years ago
- PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transiti…☆21Apr 30, 2026Updated 3 months ago
- QUICK: A GPU-enabled ab intio quantum chemistry software package☆218Jul 25, 2026Updated 2 weeks ago
- Flexible Artificial Intelligence Docking☆19Aug 27, 2025Updated 11 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.☆61Jul 17, 2025Updated last year
- ☆25Feb 28, 2023Updated 3 years ago
- The official implementation of Energy-Inspired Molecular Conformation Optimization (ICLR 2022)☆36Oct 15, 2022Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.☆77Mar 27, 2025Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆43Apr 27, 2026Updated 3 months ago
- CREST - A program for the automated exploration of low-energy molecular chemical space.☆345Jun 16, 2026Updated last month
- Calculation of interatomic interactions in molecular structures☆139Sep 3, 2024Updated last year
- mmCIF Core Access Library☆50Updated this week
- Mirror of pDynamo computational chemistry software, which does not currently use a public version control repository☆10Feb 23, 2017Updated 9 years ago
- EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes☆18Sep 5, 2024Updated last year
- automated reaction profile generation☆209Mar 10, 2026Updated 5 months ago
- Open-source protein-based pharmacophore modeling software☆42Feb 15, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Protein Annotation by Residue-Specific Enrichment: a site-based statistical method for interpretable protein function annotation☆16Jun 16, 2025Updated last year
- An interoperable Python framework for biomolecular simulation.☆167Updated this week
- MMTSB Tool Set☆33Jan 26, 2026Updated 6 months ago
- Adaptive string method implementation in AmberTools23 and Amber22☆15Jan 7, 2025Updated last year
- A deep-learning-based multiple toolkits (DeTool) approach that uses the inputs of enzymes and substrates for biocatalystic tasks.☆14Nov 24, 2023Updated 2 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 8 months ago
- Pembrolizumab-like Antibody Hallucination using AlphaFold2☆16Nov 10, 2023Updated 2 years ago