federico-fogolari / pdb2entropyView external linksLinks
Entropy from PDB conformational ensembles
☆13Mar 28, 2024Updated last year
Alternatives and similar repositories for pdb2entropy
Users that are interested in pdb2entropy are comparing it to the libraries listed below
Sorting:
- Adaptive string method implementation in AmberTools23 and Amber22☆14Jan 7, 2025Updated last year
- The official GitHub repository for the Nature Communications paper "Computational Design of Generalist Cyclopropanases with Stereodiverge…☆13Jan 23, 2026Updated 3 weeks ago
- MoloVol is a free, cross-plattform, scientific software for volume and surface computations of single molecules and crystallographic unit…☆28Aug 17, 2025Updated 6 months ago
- ☆29May 5, 2025Updated 9 months ago
- Various scripts for quantum chemistry (mainly ORCA)☆15Feb 6, 2025Updated last year
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 6 years ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Oct 2, 2024Updated last year
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Jul 2, 2024Updated last year
- ProteinDesign with RFdiffusion and ProteinMPNN/LigandMPNN☆22Mar 6, 2025Updated 11 months ago
- Deciphering protein evolution and fitness landscapes with latent space models☆37Nov 2, 2021Updated 4 years ago
- A scoring function model based on 3D convolutional neural network for protein-ligand binding affinity prediction.☆17Oct 8, 2021Updated 4 years ago
- ☆24Aug 1, 2023Updated 2 years ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Jan 20, 2022Updated 4 years ago
- EGDB: A Comprehensive Multi-Omics Database for Energy Grasses and the Epigenomic Atlas of Pearl Millet☆41Jan 30, 2025Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Jun 8, 2024Updated last year
- Protein discovery tool for mining in the Alphafold database based on the position of few amino acids.☆29Jan 16, 2026Updated last month
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Oct 18, 2019Updated 6 years ago
- protein structure prediction with precision☆26May 14, 2024Updated last year
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆60Jan 30, 2026Updated 2 weeks ago
- Automated omics-scale protein modeling and simulation setup.☆53Sep 20, 2021Updated 4 years ago
- ☆21Nov 13, 2023Updated 2 years ago
- A tutorials suite for BioSimSpace.☆34Oct 22, 2025Updated 3 months ago
- ☆20Oct 4, 2022Updated 3 years ago
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆31Updated this week
- RXN for biochemical reactions☆73Oct 18, 2022Updated 3 years ago
- A fast, clean, and composable toolkit for molecular modeling☆39Feb 1, 2026Updated 2 weeks ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆75Jun 12, 2023Updated 2 years ago
- Python package built around protein structure and dynamics. OpenBabel-inspired objects.☆37May 23, 2025Updated 8 months ago
- AlphaFold-initiated replica exchange protein docking☆87Jun 5, 2025Updated 8 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Aug 11, 2023Updated 2 years ago
- ML-optimized library design with improved fitness and diversity for protein engineering☆36Nov 5, 2025Updated 3 months ago
- A model named ATMOL for predicting molecular property☆10May 2, 2022Updated 3 years ago
- This software package simulates the reduction of graphene oxide and calculates the optical response of the generated sp2 domains☆11Dec 22, 2016Updated 9 years ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆163Feb 1, 2026Updated 2 weeks ago
- ☆35Oct 14, 2024Updated last year
- ☆40Jul 17, 2024Updated last year
- PyChemEngg is a python-based framework to promote problem solving and critical thinking in chemical engineering.☆14Oct 26, 2021Updated 4 years ago
- ☆14Dec 18, 2024Updated last year
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆10Oct 2, 2025Updated 4 months ago