Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats, using Pymol as a module

Create pseudoatoms at the centroid of the catalytic atoms of a residue

Performs large-scale ligand identification, curation and extraction from human structures in the Protein Data Bank.

an addon to create proteins

PSIST algorithm to index and query 3D protien structures

Meta-Bio-Cargo predict #Ru-Bi-CO-S protein

This is a plugin for PyMol 2.x under Windows to find and show Ca-ion sites in a protein structure in pdb format using the Feature program.

The aim of this project is to correctly predict the con- tact types in given protein structures, which are to be pre- sented in PDB file format. MODELS: Random Forest, Neural Network, Support Vector Machine.

Python implementation of 3D Zernike moments with NumPy

In this research project a standardised AlphaFold 2-based molecular replacement strategy is developed and implemented in an existing biomolecule structure solution pipeline at MAX IV Laboratory. It can be run on high performance clusters similar to the LUNARC (https://www.lunarc.lu.se/). A standalone and implemented version of the pipeline exists.

Extension for creating visualizations of distance restraints in PyRy3D Chimera Extension

This repository contains the source code for the DebruijnExtend tool. This tool uses known secondary structures for common protein kmers to predict the most likely secondary structure. This is done using a debruijn graph approach to incorporate local homology for predicting the most probable secondary structure along a protein. Tested on mac/linux

Base package for the lecturing of LVCC module on "Computational Design of Proteins" @ Universidade de Aveiro, Portugal.

Source code and files for structural network analysis of Cas9 RNP

Structural Bioinformatics Course @UAM

Code for analysing coarse grain interaction in Protein-SSDna complexes.

This script aims at reading a given PDB file and generation dihedral angles from it.