Becksteinlab / propkatrajLinks
pKa estimates for proteins using an ensemble approach
☆29Updated 3 months ago
Alternatives and similar repositories for propkatraj
Users that are interested in propkatraj are comparing it to the libraries listed below
Sorting:
- Analysis of non-covalent interactions in MD trajectories☆63Updated 9 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆33Updated last month
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆30Updated last year
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆61Updated last year
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆32Updated last month
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆61Updated last month
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆36Updated last week
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 6 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- ☆39Updated last year
- Computational Chemistry Workflows☆55Updated 3 years ago
- ☆28Updated 5 months ago
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆43Updated 3 weeks ago
- A comprehensive toolkit for predicting free energies☆58Updated 9 months ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆41Updated last year
- Weighted Ensemble simulation framework in Python☆58Updated 2 weeks ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆86Updated 3 months ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Fully automated high-throughput MD pipeline☆81Updated last month
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Updated last year
- PyRod - Tracing water molecules in molecular dynamics simulations☆52Updated 4 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 2 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- ☆45Updated this week
- ☆25Updated last year
- Implementation of the SolTranNet tool utilizing the molecular transformer to predict aqueous solubility☆39Updated 4 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Fully automated docking pipeline (can be run in distributed environments)☆51Updated last month