Pinned Repositories
.vmd.d
VMD configuration files
AB-Bind-Database
Antibody Binding Mutational Database
add_acyl_tails_martini_2.2
atom_overlap_checker
checks for atom overlaps, and shifts any overlapping atoms
cg2at
Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)
metadynamics_analysis
A script for analysing well tempered metadynamics
openfold
Trainable PyTorch reproduction of AlphaFold 2
PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
self_assembly
automated setup of martini membranes using the self assembly method
umbrella_sampling
setting up and analysing PMFs
owenvickery's Repositories
owenvickery/cg2at
Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)
owenvickery/metadynamics_analysis
A script for analysing well tempered metadynamics
owenvickery/umbrella_sampling
setting up and analysing PMFs
owenvickery/atom_overlap_checker
checks for atom overlaps, and shifts any overlapping atoms
owenvickery/openfold
Trainable PyTorch reproduction of AlphaFold 2
owenvickery/PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
owenvickery/self_assembly
automated setup of martini membranes using the self assembly method
owenvickery/AB-Bind-Database
Antibody Binding Mutational Database
owenvickery/AbLang
AbLang: A language model for antibodies
owenvickery/add-to-beta-factor-column
adds 2nd column of input (eg. rmsf.xvg each line corresponding to residue) to beta factor column of pdb.
owenvickery/add_acyl_tails_martini_2.2
owenvickery/add_vsites
adding virtual sites to system
owenvickery/alphafold_non_docker
AlphaFold2 non-docker setup
owenvickery/AmorProt
Code for "AmorProt: Amino Acid Molecular Fingerprints Repurposing-based Protein Fingerprint" (https://doi.org/10.1021/acs.biochem.3c00253)
owenvickery/binding-ddg-predictor
open source repository
owenvickery/DACUM
The Database of binding Affinity Change Upon Mutations in protein complexes
owenvickery/dynamics_protein
writes out rmsd and rmsf to protein bfac
owenvickery/Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
owenvickery/google-research
Google Research
owenvickery/Martini3-small-molecules
Martini 3 small-molecule database
owenvickery/masterclass-21-4
Repository of the data for PLUMED Masterclass 21.4
owenvickery/metadynminer
Package for reading, analysis and visualization of metadynamics HILLS
owenvickery/Oligomerization-State_and_Contact-Map
owenvickery/propka
PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
owenvickery/Pros-GNN
owenvickery/PyLipID
A python toolkit for analysing membrane protein-lipid interactions.
owenvickery/show_deformation
writes the deformation of a membrane over time, using the z coordinate height
owenvickery/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
owenvickery/TICAgg
owenvickery/Weighted_cc