Useful tools - glasgowlab/home GitHub Wiki

Bioinformatics and protein analysis tools

• ExPASy proteomics

  • ProtParam - quickly calculate your protein's MW, pI, extinction coefficient
  • PeptideCutter - predict protease cleavage sites

• Foldseek server - protein structure search

  • see also Foldmason - multiple protein structure alignment method (paper)

• PDBSum - protein/ligand visualization of structures in 3D, residue conservation, 2D structure and interaction schematic diagrams, breakdown of protein motifs and active sites

• LigPlot - 2D ligand-protein interaction diagrams

• MAGPIE to visualize and analyze lots of protein-ligand interactions at once, with tutorial

• PDB-REDO - re-refine old or otherwise non-optimal X-ray crystal structures for a better model

Protein structure/ensemble prediction

• Alphafold multimer on COSMIC2 (better than CoLab)

• AlphaFold3 server

• Biogrid - database of protein-protein interactions and evidence for these

• MSA subsampling methods to predict alternate conformations of proteins

  • AF-Cluster (paper)
  • Rubenstein method (paper)
  • Cfold (paper)

• BioEmu CoLabFold - a machine learning method to emulate MD simulations (preprint)

Protein design

• RFdiffusion CoLab - includes sequence design using ProteinMPNN and structure validation with AF2

• ProteinMPNN CoLab

• DL4Proteins Notebook Series from Gray Lab

• Robetta Server and Old Robetta Server - the old server includes legacy code for making fragment libraries, alanine scanning, and the DNA Interface Residue Scanning server