Valdes-Tresanco-MS / gmx_MMPBSALinks
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
☆287Updated 2 weeks ago
Alternatives and similar repositories for gmx_MMPBSA
Users that are interested in gmx_MMPBSA are comparing it to the libraries listed below
Sorting:
- Interface for AutoDock, molecule parameterization☆319Updated 2 weeks ago
- fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…☆425Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆200Updated 2 years ago
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆162Updated 2 weeks ago
- P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.☆370Updated last week
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆328Updated last year
- Let LLM run your MDs.☆238Updated 3 months ago
- Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting f…☆273Updated 2 years ago
- Interaction Fingerprints for protein-ligand complexes and more☆460Updated last week
- OFFICIAL: AnteChamber PYthon Parser interfacE☆241Updated 6 months ago
- Official repo of the modular BioExcel version of HADDOCK☆214Updated last week
- repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model☆277Updated this week
- Uni-Dock: a GPU-accelerated molecular docking program☆267Updated last week
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆90Updated 2 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…☆217Updated last month
- NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model☆315Updated 2 months ago
- Cloud-based molecular simulations for everyone☆461Updated last month
- Application to assign secondary structure to proteins☆231Updated 3 weeks ago
- PDBFixer fixes problems in PDB files☆609Updated last month
- Training and prediction scripts for Chemprop models trained on ADMET datasets☆249Updated 3 months ago
- Accurately speed up AutoDock Vina☆155Updated 2 years ago
- DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models☆348Updated last month
- Python3 translation of AutoDockTools☆130Updated last year
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆339Updated last week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆164Updated 4 months ago
- A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discover…☆176Updated 2 months ago
- SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction☆224Updated 2 months ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆160Updated 7 months ago
- Vina-GPU 2.0 accelerates AutoDock Vina and its related commonly derived docking methods, such as QuickVina 2 and QuickVina-W with GPUs.☆112Updated 2 years ago
- PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.☆217Updated last month