Valdes-Tresanco-MS / gmx_MMPBSA
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
☆254Updated last month
Alternatives and similar repositories for gmx_MMPBSA:
Users that are interested in gmx_MMPBSA are comparing it to the libraries listed below
- Interface for AutoDock, molecule parameterization☆250Updated this week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆188Updated last year
- fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…☆345Updated 7 months ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆227Updated 3 months ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆294Updated last year
- Interaction Fingerprints for protein-ligand complexes and more☆409Updated this week
- Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting f…☆267Updated last year
- Let LLM run your MDs.☆199Updated last month
- PDBFixer fixes problems in PDB files☆541Updated 2 months ago
- Accurately speed up AutoDock Vina☆149Updated last year
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme …☆522Updated 3 weeks ago
- P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.☆319Updated 3 weeks ago
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆144Updated 2 months ago
- NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model☆289Updated last year
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆72Updated 8 months ago
- repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model☆239Updated 11 months ago
- DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models☆277Updated 3 months ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆197Updated 2 months ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆141Updated last month
- A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discover…☆169Updated 2 weeks ago
- Application to assign secondary structure to proteins☆199Updated 3 weeks ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆143Updated this week
- Plausibility checks for generated molecule poses.☆278Updated last week
- tools for GROMACS☆110Updated 3 weeks ago
- SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction☆175Updated last month
- Uni-Dock: a GPU-accelerated molecular docking program