A python implementation of pdb2oniom for QM/MM (ONIOM) calculations
☆11Oct 2, 2025Updated 5 months ago
Alternatives and similar repositories for pdb2oniom
Users that are interested in pdb2oniom are comparing it to the libraries listed below
Sorting:
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 6 years ago
- ☆11Feb 29, 2024Updated 2 years ago
- Graphormer Based Protein Sequence Design☆26Feb 2, 2024Updated 2 years ago
- Adaptive string method implementation in AmberTools23 and Amber22☆14Jan 7, 2025Updated last year
- The App Store for VMD extensions.☆14Jan 14, 2023Updated 3 years ago
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆14Nov 14, 2025Updated 4 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☆24Sep 18, 2025Updated 6 months ago
- Collection of tools for running MD, QM, and QM/MM calculations☆20Sep 27, 2025Updated 5 months ago
- ☆23Jul 14, 2023Updated 2 years ago
- Homomer symmetry prediction from protein sequence☆43Mar 13, 2025Updated last year
- Energy minimization post-processing used in PoseBusters☆14Apr 4, 2025Updated 11 months ago
- Implementation of methods to sample from Boltzmann distributions☆21Jan 24, 2023Updated 3 years ago
- ☆17Aug 28, 2025Updated 6 months ago
- A library to align rigid molecules and clusters☆12Mar 12, 2026Updated last week
- A convinent tool to visualize AlphaFold 3 prediction results with PyMOL and matplotlib☆19May 20, 2024Updated last year
- ☆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
- ☆29Nov 2, 2023Updated 2 years ago
- a toolbox for the manipulation, modelling and analysis of molecular structures☆27Nov 27, 2025Updated 3 months ago
- QMCube: An all-purpose suite for multiscale QM/MM calculations☆13Dec 13, 2024Updated last year
- pdbx is a parser module in python for structures of the protein data bank in the mmcif format☆30Aug 9, 2024Updated last year
- Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar stru…☆27Nov 1, 2025Updated 4 months ago
- ☆36Jun 17, 2025Updated 9 months ago
- ☆21Nov 13, 2023Updated 2 years ago
- [NeurIPS 2025 spotlight] Efficient factorized variant of the IPA module.☆46Nov 14, 2025Updated 4 months ago
- scripts to find PBD structures for cancer driver proteins☆31Feb 27, 2026Updated 3 weeks ago
- Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new t…☆17Feb 12, 2026Updated last month
- Novel estimator for the change in stability upon point mutation in monomeric and multimeric proteins.☆62May 21, 2025Updated 10 months ago
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 7 months ago
- R Studio dark theme, inspired by VS Code.☆16Jan 19, 2023Updated 3 years ago
- 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…☆24Jul 28, 2024Updated last year
- Precise Generation of Conformational Ensembles for Intrinsically Disordered Proteins with IDPFold☆26Sep 13, 2024Updated last year
- Fortran bindings to the FLANN library for performing fast approximate nearest neighbor searches in high dimensional spaces.☆15Jun 29, 2025Updated 8 months ago
- 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☆38Feb 27, 2026Updated 3 weeks ago
- Repository for "Nearest neighbor search on embeddings rapidly identifies distant protein relations"☆13Apr 2, 2023Updated 2 years ago
- Baseline model for PPB-Affinity benchmark data☆36May 21, 2025Updated 10 months ago