federico-fogolari / pdb2entropyLinks
Entropy from PDB conformational ensembles
☆8Updated last year
Alternatives and similar repositories for pdb2entropy
Users that are interested in pdb2entropy are comparing it to the libraries listed below
Sorting:
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆15Updated 3 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 2 weeks ago
- A tutorials suite for BioSimSpace.☆25Updated 2 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆17Updated 2 years ago
- ☆25Updated last year
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 10 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆50Updated 3 months ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated last month
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆37Updated 11 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Updated 4 years ago
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆29Updated 4 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated last year
- Machine Learning model for molecular micro-pKa prediction☆42Updated 9 months ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆14Updated last year
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- ☆65Updated last year
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 2 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆22Updated 10 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆14Updated 2 months ago
- ☆31Updated last year