GRASP-Func: Function sorting with local graph representation

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

Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.org

TMvisDB provides per-residue transmembrane topology annotations for all proteins in AlphaFold DB (~ 200 million proteins, September '22) predicted as transmembrane proteins (~ 46 million).

A Tufts Research Technology Workshop detailing how to use AlphaFold 2 on the Tufts HPC cluster

A transformer network trained to predict end-to-end single sequence protein structure as a set of angles given amino acid sequences.

The protein secondary structure classifier with 3 classes H/E/C (R implementation). Tertiary classifier is composed of binary classifiers using the combining scheme.

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

an addon to create proteins

PSIST algorithm to index and query 3D protien structures

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

A script to obtain a difference distance matrix.

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.

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.

Python implementation of 3D Zernike moments with NumPy

Superpose3D is a software for local comparison of protein structures that allows for user-defined structure representations

Implementation of the Ant Colony Optimization meta-heuristic for the Protein Structure Prediction problem using 2D HP model. This approach includes the pull move heuristic for local search.