Abysis is a complete system for loading, storing and analysing public and proprietary antibody sequences and 3D structures. The loading software pairs light and heavy chains and ensures that all antibody sequences are numbered in the universally recognised forms (such as Kabat or Chothia). It then performs other key assessments prior to loading into an SQL database. The interface provides many key facilities including the analysis of residue and length distributions as well as a number of antibody-specific sequence analysis tools.
Developed at UCL by Simon Hubbard and Janet Thornton, this program calculates absolute and relative surface accessibilities of protein and nucleic acid structures. The program can also be used in conjunction with the Ligplot program to provide information on buried and accessible residues.
Academic researchers: a non-commercial use only licence for academic researchers is available from the following website: www.bioinf.manchester.ac.uk/naccess/
PDBsum, one of the world’s foremost web sites for viewing and interrogating protein structures deposited in the Protein Data Bank (PDB), is now available as in-house product PDBsumProprietary, to allow companies to organise their internal proprietary protein structure data. PDBsum originated at University College London (UCL) in the Biomolecular Structure group. The system was developed by Dr. Roman Laskowski, now at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK.
[The public web-based version is available at http://www.ebi.ac.uk/pdbsum/]