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haddock3

The official repo of the new modular BioExcel2 version of HADDOCK

ibm3202

Google Colab Tutorials for IBM3202

interactiverosetta

A wxPython graphical interface for the PyRosetta and Rosetta protein modeling suites

intpred

iscore

iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines

isee

libzdock

ZDOCK predictions and PDB structures in C++ and Python

lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

llamanade

localcolabfold

ColabFold on your local PC

making-it-rain

Cloud-based molecular simulations for everyone

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

mdms

MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins

mdnotebooks

Jupyter Notebooks for Molecular Dynamics

meetdock

Protein-Protein Docking software

megadock-on-colab

MEGADOCK on Google Colaboratory

molecular-dynamics

move-wsl

Easily move your WSL distros VHDX file to a new location.

mutabindv2.0

dataset for MutaBindv2.0

mutatex

scripts and facilities for in-silico mutagenesis with FoldX

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

pdbfixer

PDBFixer fixes problems in PDB files

pdbremix

analyse PDB files, run molecular-dynamics & analyse trajectories

pecan

Help file for running the scripts to learn and evaluate graph convolution networks for epitope and paratope prediction

pignet

PIGNet source code

prodigy

Repository containing various scripts to predict the binding affinity of protein-protein complexes from structure

propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

proqdock

ProQDock is a Protein-Protein docking scoring program that uses high level coordinate driven features compiled and trained by a Support Vector Regression algorithm. The current version has 13 features: both all-atom and interface features. ProQDock should also serve to develop hybrid methods in future attempts to solve this 'hard' problem.

protein-indelmaker

protparamwrap

wrapper to submit multiple sequences to analyze with protParam tool