A python implementation of pdb2oniom for QM/MM (ONIOM) calculations
☆12Oct 2, 2025Updated 9 months ago
Alternatives and similar repositories for pdb2oniom
Users that are interested in pdb2oniom are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 7 years ago
- ☆10Feb 29, 2024Updated 2 years ago
- Graphormer Based Protein Sequence Design☆26Feb 2, 2024Updated 2 years ago
- Adaptive string method implementation in AmberTools23 and Amber22☆15Jan 7, 2025Updated last year
- The App Store for VMD extensions.☆14Jan 14, 2023Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆13Nov 14, 2025Updated 7 months ago
- QM/MM interfacing in Python☆10Feb 12, 2019Updated 7 years ago
- code and source data for de novo design of Kemp elimination paper☆26Sep 18, 2025Updated 9 months ago
- ☆22Jul 14, 2023Updated 2 years ago
- Collection of tools for running MD, QM, and QM/MM calculations☆21Sep 27, 2025Updated 9 months ago
- Energy minimization post-processing used in PoseBusters☆14Apr 4, 2025Updated last year
- Homomer symmetry prediction from protein sequence☆45Mar 13, 2025Updated last year
- Implementation of methods to sample from Boltzmann distributions☆22Jan 24, 2023Updated 3 years ago
- ☆18Aug 28, 2025Updated 10 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A library to align rigid molecules and clusters☆13Jun 19, 2026Updated last week
- A convinent tool to visualize AlphaFold 3 prediction results with PyMOL and matplotlib☆19May 20, 2024Updated 2 years ago
- ☆40Jul 17, 2024Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆118Dec 29, 2018Updated 7 years ago
- Docking Tool Benchmarking Workflow☆25Jul 17, 2024Updated last year
- a toolbox for the manipulation, modelling and analysis of molecular structures☆28Nov 27, 2025Updated 7 months ago
- QMCube: An all-purpose suite for multiscale QM/MM calculations☆13Dec 13, 2024Updated last year
- ☆32Nov 2, 2023Updated 2 years ago
- pdbx is a parser module in python for structures of the protein data bank in the mmcif format☆31Aug 9, 2024Updated last year
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- ☆40Jun 17, 2025Updated last year
- Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar stru…☆30May 15, 2026Updated last month
- ☆22Nov 13, 2023Updated 2 years ago
- [NeurIPS 2025 spotlight] Efficient factorized variant of the IPA module.☆48Nov 14, 2025Updated 7 months ago
- scripts to find PBD structures for cancer driver proteins☆31Feb 27, 2026Updated 4 months ago
- Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new t…☆17Jun 23, 2026Updated last week
- Novel estimator for the change in stability upon point mutation in monomeric and multimeric proteins.☆64May 21, 2025Updated last year
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 11 months ago
- R Studio dark theme, inspired by VS Code.☆16Jan 19, 2023Updated 3 years ago
- 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.
- Precise Generation of Conformational Ensembles for Intrinsically Disordered Proteins with IDPFold☆27Sep 13, 2024Updated last year
- Academic license pre-required. While FEP Plus charge you 100,000 USD per year. Here comes the FEP-Minus, it is a Schrodinger FEP Plus ide…☆25Jul 28, 2024Updated last year
- Fortran bindings to the FLANN library for performing fast approximate nearest neighbor searches in high dimensional spaces.☆15Jun 29, 2025Updated last year
- Map genetic variants and protein positions to protein interfaces in 3D☆13Sep 22, 2023Updated 2 years ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆41Jun 19, 2026Updated last week
- Repository for "Nearest neighbor search on embeddings rapidly identifies distant protein relations"☆13Apr 2, 2023Updated 3 years ago
- bakerlab pymol scripts☆27Feb 6, 2020Updated 6 years ago