patcHwork
Impressum - Contact
Version 1.1a
  • Welcome to patcHwork
  • patcHwork is a user-friendly web-server that identifies amino acids of proteins that undergo a charge-shift when the pH assumes two user-defined values. For sequence functionality, users may submit a FASTA file with up to ten thousand amino acid sequences (max 20MB). For structure functionality, users may submit a single 3D structure (PDB) file or a zip file with multiple PDB files (max 20MB) for batch processing.

    patcHwork is free and open to all users and there is no login requirement.




    To gain a deeper mechanistic understanding of the effect of pH changes on a protein of interest, patcHwork performs an analysis on submitted 3D protein structures using the PDB2PQR and PROPKA tools. The graphic user interface of patcHwork makes it possible to easily locate pH-sensitive residues on the protein structure at two defined pH values as well as to visualize salt bridges, hydrogen bonds and aromatic interactions that change upon pH shift. Furthermore, patcHwork offers the possibility to identify patches of pH-sensitive residues that are in close proximity on the protein structure, as they are likely to have a major impact on protein activity.
  • Additional information
  • Citation:
    patcHwork: A user friendly pH sensitivity analysis web-server for protein sequences and structures. Mirko Schmitz, Anne Schultze, Raimonds Vanags, Karsten Voigt, Barbara Di Ventura, Mehmet Ali Öztürk

    References:
    PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
    Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens E. Nielsen, Jan H. Jensen, Gerhard Klebe, and Nathan A. Baker's Nucleic Acids Res. 2007 35 (Web Server issue), W522-5.
    PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions
    Mats H. M. Olsson, Chresten R. Søndergaard, Michal Rostkowski, and Jan H. Jensen Journal of Chemical Theory and Computation 2011 7 (2), 525-537
    NGL viewer: web-based molecular graphics for large complexes
    Alexander S Rose, Anthony R Bradley, Yana Valasatava, Jose M Duarte, Andreas Prlić, and Peter W Rose Bioinformatics 2018, 34 (21), 3755-3758
    Derivation and use of a formula to calculate the net charge of acid-base compounds. Its application to amino acids, proteins and nucleotides
    José C. Cameselle, João Meireles Ribeiro, and Antonio Sillero Biochemical Education 1986, 14 (3), 131-136

    CIBSS UniFreiburg BIOSS Erc bmbf