federico-fogolari / pdb2entropy
Entropy from PDB conformational ensembles
☆8Updated 7 months ago
Related projects ⓘ
Alternatives and complementary repositories for pdb2entropy
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆30Updated 8 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆27Updated 4 months ago
- ☆25Updated 9 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 10 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆13Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆13Updated last year
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- Different run and analysis scripts as described in the research guides.☆10Updated 2 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆20Updated last year
- A middleware python tool for computational drug discovery on HPC architectures☆9Updated 8 months ago
- ☆29Updated 3 weeks ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated last year
- ☆26Updated 10 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 2 months ago
- ☆25Updated 3 weeks ago
- A tutorials suite for BioSimSpace.☆16Updated last week
- Automate MD associated calculations☆29Updated 3 weeks ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆10Updated 2 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆11Updated last week
- ☆27Updated 5 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆27Updated last week
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆15Updated 4 months ago
- ☆10Updated 4 months ago
- Collection of Python scripts to setup and run simulations with OpenMM☆14Updated 4 years ago
- Temperature generator for Replica Exchange MD simulations☆25Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆43Updated this week
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆15Updated last week