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The AAAAA aims to become the ultimate tool for antibody structural analysis, modelling and engineering
Its unifying theme of this site is the structural alignment of antibody and Tcell receptor sequences. To simplify handling of the information, two important rules have been rigorously followed:
All sequences, be it VH, Vk, Va, Vb, Vg or Vd are numbered in an identical way. As the numbering is based on the structural alignment, residues with the same residue number are in structurally equivalent position. Conversly, structurally equivalent residues will always have the same residue number.
The antibody and TCR coordinate files from the PDB have been dissected into individual domains and reoriented to provide a structural superposition. These files can be downloaded individually or all together as a compressed archive
The key tools provided in the AAAAA website are:
The EXCEL macros provided on this server allow to, e.g.:
  • read sequences and sequence alignments into an EXCEL file
  • color-code this sequence alignment according to different properties which can be derived from the sequence alignment itself, such as amino acid type, hydrophobicity, similarity to a reference sequence.
  • derive sequence statistics from a sequence alignement
  • color code the sequence according to properties listed in separate files, such as residue accessibility, differences in residue accessibility (to identify interactions), unusual torsion angles, structural deviation from a reference structure
  • import coordinate files, renumber them according to the new AHo consensus and re-export them
  • Analyze H-Bond pattern and torsion angles imported from other programs
So What?
What can you do with AAAAA? Here are just a few examples of everyday tasks, which can now be done in minutes:
  • Check your antibody sequence for plausibility. Any really unusual residues? Sequencing mistakes? Frameshifts? Insertions and deletions?
  • Find the closest solved structure
  • Find the closest germline sequence and any likely somatic mutations
  • Find the most likely antigen contacts, depending on whether your antigen is a hapten, peptide or protein
  • What is the probability of finding a given amino acid type in a given position?
  • Check structure/function correllations: As a statistical analysis for every residue is available, its position in the structure can immediatly be checked, before even doing any modelling. Is it exposed or buried? Is it likely to participate in an interface? Hydrogen-bonded?
  • Find trouble spots: Your antibody is misbehaving. Maybe it is lacking a crucial ionic interaction or has a residue unhappy about its phi/psi angle constraints? An analysis will tell immediately
  • We think that the greatest advantage of this site is that in each and every structure, superimposed residues have the the same residue number. Therefore, you can click on a sequence position and find out that its environment looks like in all domains. A comparison of TCRs and antibodies , e.g., is very easy, because the have allready been aligned and superimposed.
Please note that this in an ongoing project. Besides adding to the static content offered at the moment, we plan to offer a variety of fully web-based services. Check back frequently and tell us what you think about the database and tools you would like to find in this ressource.
We are also working on compiling a database of the effects of individual point mutations and combinations of mutations on the stability, folding efficency and production yields of engineered antibody fragments. Based on this data, we plan to produce a "checklist" of potentially beneficial mutations. If you have any experimental data of this kind to share, whether quantitative or just qualitative, we are grateful for your contribution.
Feel like you even want to join the lab and work on improving AAAAA?
Check with Andreas Plückthun or Annemarie Honegger
AAAAA Homepage Zürich University Dept. of Biochemistry Plückthun Group Annemarie Honegger

Last Modified by A.Honegger Tuesday, January 25, 2005