hugecadd / PiViewer
PiViewer: an open-source tool for automated detection and display of pi-pi interactions
☆13Updated 6 years ago
Alternatives and similar repositories for PiViewer:
Users that are interested in PiViewer are comparing it to the libraries listed below
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆12Updated 4 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆22Updated 2 years ago
- ☆28Updated last year
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆16Updated this week
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆15Updated last year
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆27Updated 8 months ago
- Automated construction of protein chimeras and their analysis.☆14Updated last year
- Tutorial to build AMBER compatable protein+lipid systems☆14Updated 7 years ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆17Updated 4 years ago
- bakerlab pymol scripts☆21Updated 5 years ago
- Software package for FEP☆18Updated 8 months ago
- ☆25Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 4 months ago
- Extract ligand binding sites from PDB. Match the binding sites to de novo scaffolds.☆11Updated 4 years ago
- Software for the prediction of DEER and PRE data from conformational ensembles.☆12Updated 6 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆16Updated 4 years ago
- An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM☆36Updated 7 months ago
- Automatic CHARMM-GUI browser interaction with Python☆13Updated 2 years ago
- MD pharmacophores and virtual screening☆33Updated last year
- This repo contains the collection of codes to find designer interfacial mutations☆17Updated last year
- ☆11Updated 9 months ago
- Fully automated high-throughput MD pipeline☆57Updated this week
- For the purpose of post progressing of MD carried by gromacs☆20Updated last week
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆15Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆31Updated last month
- ☆32Updated 11 months ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆20Updated 5 years ago