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.
☆264Updated 3 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:
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆190Updated last year
- Interface for AutoDock, molecule parameterization☆257Updated 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…☆356Updated 9 months ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆229Updated last week
- Interaction Fingerprints for protein-ligand complexes and more☆421Updated this week
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆301Updated last year
- A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discover…☆172Updated 2 months ago
- P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.☆329Updated this week
- Let LLM run your MDs.☆211Updated 2 months ago
- NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model☆291Updated last year
- Official repo of the modular BioExcel version of HADDOCK☆167Updated this week
- DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models☆287Updated 4 months ago
- Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting f…☆268Updated last year
- Accurately speed up AutoDock Vina☆152Updated last year
- repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model☆252Updated last year
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆148Updated 3 months ago
- PDBFixer fixes problems in PDB files☆548Updated 3 months ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆306Updated last month
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆202Updated last week
- Protein-ligand structure prediction☆217Updated 10 months ago
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆74Updated 10 months ago
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme …☆548Updated last month
- Cloud-based molecular simulations for everyone☆437Updated last week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆150Updated last month
- Public RFDiffusionAA repo☆399Updated 11 months ago
- ChatMol☆230Updated 3 months ago
- Uni-Dock: a GPU-accelerated molecular docking program☆235Updated 2 months ago
- Application to assign secondary structure to proteins☆201Updated last week
- Plausibility checks for generated molecule poses.☆289Updated 3 weeks ago
- In silico directed evolution of peptide binders with AlphaFold☆199Updated last week